Intracellular signaling molecules

ABSTRACT

Various embodiments of the invention provide human intracellular signaling molecules (INTSIG) and polynucleotides which identify and encode INTSIG. Embodiments of the invention also provide expression vectors, host cells, antibodies, agonists, and antagonists. Other embodiments provide methods for diagnosing, treating, or preventing disorders associated with aberrant expression of INTSIG.

TECHNICAL FIELD

The invention relates to novel nucleic acids, intracellular signaling molecules encoded by these nucleic acids, and to the use of these nucleic acids and proteins in the diagnosis, treatment, and prevention of cell proliferative, endocrine, autoimmune/inflammatory, neurological, gastrointestinal, reproductive, developmental, and vesicle trafficking disorders. The invention also relates to the assessment of the effects of exogenous compounds on the expression of nucleic acids and intracellular signaling molecules.

BACKGROUND OF THE INVENTION

Cell-cell communication is essential for the growth, development, and survival of multicellular organisms. Cells communicate by sending and receiving molecular signals. An example of a molecular signal is a growth factor, which binds and activates a specific transmembrane receptor on the surface of a target cell. The activated receptor transduces the signal intracelularly, thus initiating a cascade of biochemical reactions that ultimately affect gene transcription and cell cycle progression in the target cell.

Intracellular signaling is the process by which cells respond to extracellular signals (hormones, neurotransmitters, growth and differentiation factors, etc.) through a cascade of biochemical reactions that begins with the binding of a signaling molecule to a cell membrane receptor and ends with the activation of an intracellular target molecule. Intermediate steps in the process involve the activation of various cytoplasmic proteins by phosphorylation via protein kinases, and their deactivation by protein phosphatases, and the eventual translocation of some of these activated proteins to the cell nucleus where the transcription of specific genes is triggered. The intracellular signaling process regulates all types of cell functions including cell proliferation, cell differentiation, and gene transcription, and involves a diversity of molecules including protein kinases and phosphatases, and second messenger molecules such as cyclic nucleotides, calcium-calmodulin, inositol and various mitogens that regulate protein phosphorylation.

A distinctive class of signal transduction molecules are involved in odorant detection. The process of odorant detection involves specific recognition by odorant receptors. The olfactory mucosa also appears to possess an additional group of odorant-binding proteins which recognize and bind separate classes of odorants. For example, cDNA clones from rat have been isolated which correspond to mRNAs highly expressed in olfactory mucosa but not detected in other tissues. The proteins encoded by these clones are homologous to proteins that bind lipopolysaccharides or polychlorinated biphenyls, and the different proteins appear to be expressed in specific areas of the mucosal tissue. These proteins are believed to interact with odorants before or after specific recognition by odorant receptors, perhaps acting as selective signal filters (Dear, T. N. et al. (1991) EMBO J. 10:2813-2819; Vogt, R. G. et al (1991) J. Neurobiol. 22:74-84).

Cells also respond to changing conditions by switching off signals. Many signal transduction proteins are short-lived and rapidly targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Cells also maintain mechanisms to monitor changes in the concentration of denatured or unfolded proteins in membrane-bound extracytoplasmic compartments, including a transmembrane receptor that monitors the concentration of available chaperone molecules in the endoplasmic reticulum and transmits a signal to the cytosol to activate the transcription of nuclear genes encoding chaperones in the endoplasmic reticulum.

Certain proteins in intracellular signaling pathways serve to link or cluster other proteins involved in the signaling cascade. These proteins are referred to as scaffold, anchoring, or adaptor proteins. (For review, see Pawson, T. and J. D. Scott (1997) Science 278:2075-2080.) As many intracellular signaling proteins such as protein kinases and phosphatases have relatively broad substrate specificities, the adaptors help to organize the component signaling proteins into specific biochemical pathways. Many of the above signaling molecules are characterized by the presence of particular domains that promote protein-protein interactions. A sampling of these domains is discussed below, along with other important intracellular messengers.

Intracellular Signaling Second Messenger Molecules

Protein Phosphorylation

Protein kinases and phosphatases play a key role in the intracellular signaling process by controlling the phosphorylation and activation of various signaling proteins. The high energy phosphate for this reaction is generally transferred from the adenosine triphosphate molecule (ATP) to a particular protein by a protein kinase and removed from that protein by a protein phosphatase. Protein kinases are roughly divided into two groups: those that phosphorylate serine or threonine residues (serine/threonine kinases, STK) and those that phosphorylate tyrosine residues (protein tyrosine kinases, PTK). A few protein kinases have dual specificity for serine/threonine and tyrosine residues. Almost all kinases contain a conserved 250-300 amino acid catalytic domain containing specific residues and sequence motifs characteristic of the kinase family (Hardie, G. and S. Hanks (1995) The Protein Kinase Facts Books, Vol I:7-20, Academic Press, San Diego, Calif.).

STKs include the second messenger dependent protein kinases such as the cyclic-AMP dependent protein kinases (PKA), involved in mediating hormone-induced cellular responses; calcium-calmodulin (CaM) dependent protein kinases, involved in regulation of smooth muscle contraction, glycogen breakdown, and neurotransmission; and the mitogen-activated protein kinases (MAP kinases) which mediate signal transduction from the cell surface to the nucleus via phosphorylation cascades. Altered PKA expression is implicated in a variety of disorders and diseases including cancer, thyroid disorders, diabetes, atherosclerosis, and cardiovascular disease (Isseroacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, New York, N.Y.; pp. 416-431, 1887).

PTKs are divided into transmembrane, receptor PTKs and nontransmembrane, non-receptor PTKs. Transmembrane PTKs are receptors for most growth factors. Non-receptor PTKs lack transmembrane regions and, instead, form complexes with the intracellular regions of cell surface receptors. Receptors that function through non-receptor PTKs include those for cytokines and hormones (growth hormone and prolactin) and antigen-specific receptors on T and B lymphocytes. Many of these PTKs were first identified as the products of mutant oncogenes in cancer cells in which their activation was no longer subject to normal cellular controls. In fact, about one third of the known oncogenes encode PTKs, and it is well known that cellular transformation (oncogenesis) is often accompanied by increased tyrosine phosphorylation activity (Charbonneau H. and N. K. Tonks (1992) Annu. Rev. Cell Biol. 8:463-493).

An additional family of protein kinases previously thought to exist only in prokaryotes is the histidine protein kinase family (HPK). HPKs bear little homology with mammalian STKs or PTKs but have distinctive sequence motifs of their own (Davie, J. R et al. (1995) J. Biol. Chem. 270:19861-19867). A histidine residue in the N-terminal half of the molecule (region I) is an autophosphorylation site. Three additional motifs located in the C-terminal half of the molecule include an invariant asparagine residue in region II and two glycine-rich loops characteristic of nucleotide binding domains in regions III and IV. Recently a branched chain alpha-ketoacid dehydrogenase kinase has been found with characteristics of HPK in rat (Davie et al., supra).

Protein phosphatases regulate the effects of protein kinases by removing phosphate groups from molecules previously activated by kinases. The two principal categories of protein phosphatases are the protein (serine/threonine) phosphatases (PPs) and the protein tyrosine phosphatases (PTPs). PPs dephosphorylate phosphoserine/threonine residues and are important regulators of many cAMP-mediated hormone responses (Cohen, P. (1989) Annu. Rev. Biochem 58:453-508). PTPs reverse the effects of protein tyrosine kinases and play a significant role in cell cycle and cell signaling processes (Charbonneau and Tonks, supra). As previously noted, many PTKs are encoded by oncogenes, and oncogenesis is often accompanied by increased tyrosine phosphorylation activity. It is therefore possible that PTPs may prevent or reverse cell transformation and the growth of various cancers by controlling the levels of tyrosine phosphorylation in cells. This hypothesis is supported by studies showing that overexpression of PTPs can suppress transformation in cells, and that specific inhibition of PTPs can enhance cell transformation (Charbonneau and Tonks, supra).

Phospholipid and Inositol-Phosphate Signaling

Inositol phospholipids (phosphoinositides) are involved in an intracellular signaling pathway that begins with binding of a signaling molecule to a G-protein linked receptor in the plasma membrane. This leads to the phosphorylation of phosphatidylinositol (PI) residues on the inner side of the plasma membrane to the biphosphate state (PIP₂) by inositol kinases. Simultaneously, the G-protein linked receptor binding stimulates a trimeric G-protein which in turn activates a phosphoinositide-specific phospholipase C-β. Phospholipase C-β then cleaves PIP₂ into two products, inositol triphosphate (IP₃) and diacylglycerol. These two products act as mediators for separate signaling events. IP₃ diffuses through the plasma membrane to induce calcium release from the endoplasmic reticulum (ER), while diacylglycerol remains in the membrane and helps activate protein kinase C, a serine-threonine kinase that phosphorylates selected proteins in the target cell. The calcium response initiated by IP₃ is terminated by the dephosphorylation of IP₃ by specific inositol phosphatases. Cellular responses that are mediated by this pathway are glycogen breakdown in the liver in response to vasopressin, smooth muscle contraction in response to acetylcholine, and thrombin-induced platelet aggregation.

Inositol-phosphate signaling controls tubby, a membrane bound transcriptional regulator that serves as an intracellular messenger of Gα_(q)-coupled receptors (Santagata et al (2001) Science 292:2041-2050). Members of the tubby family contain a C-terminal tubby domain of about 260 amino acids that binds to double-stranded DNA and an N-terminal transcriptional activation domain. Tubby binds to phosphatidylinositol 4,5-bisphosphate, which localizes tubby to the plasma membrane. Activation of the G-protein α_(q) leads to activation of phospholipase C-β and hydrolysis of phosphoinositide. Loss of phosphatidylinositol 4,5-bisphosphate causes tubby to dissociate from the plasma membrane and to translocate to the nucleus where tubby regulates transcription of its target genes. Defects in the tubby gene are associated with obesity, retinal degeneration, and hearing loss (Boggon, T. J. et al. (1999) Science 286:2119-2125).

Cyclic Nucleotide Signaling

Cyclic nucleotides (cAMP and cGMP) function as intracellular second messengers to transduce a variety of extracellular signals including hormones, light, and neurotransmitters. In particular, cyclic-AMP dependent protein kinases (PKA) are thought to account for all of the effects of cAMP in most mammalian cells, including various hormone-induced cellular responses. Visual excitation and the phototransmission of light signals in the eye is controlled by cyclic-GMP regulated, Ca²⁺-specific channels. Because of the importance of cellular levels of cyclic nucleotides in mediating these various responses, regulating the synthesis and breakdown of cyclic nucleotides is an important matter. Thus adenylyl cyclase, which synthesizes cAMP from AMP, is activated to increase cAMP levels in muscle by binding of adrenaline to β-adrenergic receptors, while activation of guanylate cyclase and increased cGMP levels in photoreceptors leads to reopening of the Ca²⁺-specific channels and recovery of the dark state in the eye. There are nine known transmembrane isoforms of mammalian adenylyl cyclase, as well as a soluble form preferentially expressed in testis. Soluble adenylyl cyclase contains a P-loop, or nucleotide binding domain, and may be involved in male fertility (Buck, J. et al. (1999) Proc. Natl. Acad. Sci. USA 96:79-84).

In contrast, hydrolysis of cyclic nucleotides by cAMP and cGMP-specific phosphodiesterases (PDEs) produces the opposite of these and other effects mediated by increased cyclic nucleotide levels. PDEs appear to be particularly important in the regulation of cyclic nucleotides, considering the diversity found in this family of proteins. At least seven families of mammalian PDEs (PDE1-7) have been identified based on substrate specificity and affinity, sensitivity to cofactors, and sensitivity to inhibitory drugs (Beavo, J. A. (1995) Physiol. Rev. 75:725-748). PDE inhibitors have been found to be particularly useful in treating various clinical disorders. Rolipram, a specific inhibitor of PDE4, has been used in the treatment of depression, and similar inhibitors are undergoing evaluation as anti-inflammatory agents. Theophylline is a nonspecific PDE inhibitor used in the treatment of bronchial asthma and other respiratory diseases (Banner, K. H. and C. P. Page (1995) Eur. Respir. J. 8:996-1000).

Calcium Signaling Molecules

Ca²⁺ is another second messenger molecule that is even more widely used as an intracellular mediator than cAMP. Ca²⁺ can enter the cytosol by two pathways, in response to extracellular signals. One pathway acts primarily in nerve signal transduction where Ca²⁺ enters a nerve terminal through a voltage-gated Ca²⁺ channel The second is a more ubiquitous pathway in which Ca²⁺ is released from the ER into the cytosol in response to binding of an extracellular signaling molecule to a receptor. Ca²⁺ directly activates regulatory enzymes, such as protein kinase C, which trigger signal transduction pathways. Ca²⁺ also binds to specific Ca²⁺-binding proteins (CBPs) such as calmodulin (CaM) which then activate multiple target proteins in the cell including enzymes, membrane transport pumps, and ion channels. CaM interactions are involved in a multitude of cellular processes including, but not limited to, gene regulation, DNA synthesis, cell cycle progression, mitosis, cytokinesis, cytoskeletal organization, muscle contraction, signal transduction, ion homeostasis, exocytosis, and metabolic regulation (Celio, M. R. et al (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, Oxford, UK, pp. 15-20). Some Ca²⁺ binding proteins are characterized by the presence of one or more EF-hand Ca²⁺ binding motifs, which are comprised of 12 amino acids flanked by α-helices (Celio, supra). The regulation of CBPs has implications for the control of a variety of disorders. Calcineurin, a CaM-regulated protein phosphatase, is a target for inhibition by the immunosuppressive agents cyclosporin and FK506. This indicates the importance of calcineurin and CaM in the immune response and immune disorders (Schwaninger M. et al. (1993) J. Biol Chem. 268:23111-23115). The level of CaM is increased several-fold in tumors and tumor-derived cell lines for various types of cancer (Rasmussen, C. D. and A. R. Means (1989) Trends Neurosci. 12:433-438).

The annexins are a family of calcium-binding proteins that associate with the cell membrane (Towle, C. A. and B. V. Treadwell (1992) J. Biol. Chem. 267:5416-5423). Annexins reversibly bind to negatively charged phospholipids (phosphatidylcholine and phosphatidylserine) in a calcium dependent manner. Annexins participate in various processes pertaining to signal transduction at the plasma membrane, including membrane-cytoskeleton interactions, phospholipase inhibition, anticoagulation, and membrane fusion. Annexins contain four to eight repeated segments of about 60 residues. Each repeat folds into five alpha helices wound into a right-handed superhelix.

G-Protein Signaling

Guanine nucleotide binding proteins (G-proteins) are critical mediators of signal transduction between a particular class of extracellular receptors, the G-protein coupled receptors (GPCRs), and intracellular second messengers such as cAMP and Ca²⁺. G-proteins are linked to the cytosolic side of a GPCR such that activation of the GPCR by ligand binding stimulates binding of the G-protein to GTP, inducing an “active” state in the G-protein. In the active state, the G-protein acts as a signal to trigger other events in the cell such as the increase of cAMP levels or the release of Ca²⁺ into the cytosol from the ER, which, in turn, regulate phosphorylation and activation of other intracellular proteins. Recycling of the G-protein to the inactive state involves hydrolysis of the bound GTP to GDP by a GTPase activity in the G-protein. (See Alberts, B. et al. (1994) Molecular Biology of the Cell Garland Publishing, Inc. New York, N.Y., pp.734-759.) The superfamily of G-proteins consists of several families which maybe grouped as translational factors, heterotrimeric G-proteins involved in transmembrane signaling processes, and low molecular weight (LMW) G-proteins including the proto-oncogene Ras proteins and products of rab, rap, rho, rac, smg21, smg25, YPT, SEC4, and ARF genes, and tubulins (Kaziro, Y. et al (1991) Annu. Rev. Biochem. 60:349-400). In all cases, the GTPase activity is regulated through interactions with other proteins. G protein activity is triggered by seven-transmembrane cell surface receptors (G-protein coupled receptors) which respond to lipid analogs, amino acids and their derivatives, peptides, cytokines, and specialized stimuli such as light, taste, and odor. Activation of the receptor by its stimulus causes the replacement of the G protein-bound GDP with GTP. Gα-GTP dissociates from the receptor/βγ complex, and each of these separated components can interact with and regulate downstream effectors. The signaling stops when Gα hydrolyzes its bound GTP to GDP and reassociates with the βγ complex (Neer, supra).

Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP. This intrinsic GTase activity of ras is stimulated by a family of proteins collectively known as ‘GAP’ or GTPase-activating proteins. Since the GTP bound form of ras is active, ras-GAP proteins down-regulate ras. ras Gap is an alpha-helical domain that accelerates the GTPase activity of Ras, thereby “switching” it into an “off” position (Wittinghofer, A. et al. (1997) FEBS Lett. 410:63-67)

Guanine nucleotide binding proteins (GTP-binding proteins) participate in a wide range of regulatory functions in all eukaryotic cells, including metabolism, cellular growth, differentiation, signal transduction, cytoskeletal organization, and intracellular vesicle transport and secretion. In higher organisms they are involved in signaling that regulates such processes as the immune response (Aussel, C. et al. (1988) J. Immunol. 140:215-220), apoptosis, differentiation, and cell proliferation including oncogenesis (Dhanasekaran, N. et al. (1998) Oncogene 17:1383-1394). Exchange of bound GDP for GTP followed by hydrolysis of GTP to GDP provides the energy that enables GTP-binding proteins to alter their conformation and interact with other cellular components. The superfamily of GTP-binding proteins consists of several families and may be grouped as translational factors, heterotrimeric GTP-binding proteins involved in transmembrane signaling processes (also called G-proteins), and low molecular weight (LMW) GTP-binding proteins including the proto-oncogene Ras proteins and products of rab, rap, rho, rac, smg21, smg25, YPT, SEC4, and ARF genes, and tubulins (Kaziro, Y. et al. (1991) Annu. Rev. Biochem. 60:349-400). In all cases, the GTPase activity is regulated through interactions with other proteins.

The low molecular weight ([MW) GTP-binding proteins regulate cell growth, cell cycle control, protein secretion, and intracellular vesicle interaction. These GTP-binding proteins respond to extracellular signals from receptors and activating proteins by transducing mitogenic signals (Tavitian, A. (1995) C. R. Seances Soc. Biol Fil. 189:7-12). Low molecular weight GTP-binding proteins consist of single polypeptides of 21-30 kD which are able to bind to and hydrolyze GTP, thus cycling from an inactive to an active state.

Low molecular weight GTP-binding proteins play critical roles in cellular protein trafficking events, such as the translocation of proteins and soluble complexes from the cytosol to the membrane through an exchange of GDP for GTP (Ktistakis, N. T. (1998) BioEssays 20:495-504). In vesicle transport, the interaction between vesicle- and target-specific identifiers (v-SNAREs and tSNAREs) docks the vesicle to the acceptor membrane. The budding process is regulated by GTPases such as the closely related ADP ribosylation factors (ARFs) and SAR proteins, while GTPases such as Rab allow assembly of SNARE complexes and may play a role in removal of defective complexes (Rothman, J. E. and F. T. Wieland (1996) Science 272:227-234). The rab proteins control the translocation of vesicles to and from membranes for protein localization, protein processing, and secretion. The rho GTP-binding proteins control signal transduction pathways that link growth factor receptors to actin polymerization which is necessary for normal cellular growth and division. The ran GTP-binding proteins are located in the nucleus of cells and have a key role in nuclear protein import, the control of DNA synthesis, and cell-cycle progression (Hall, A. (1990) Science 249:635-640; Scheffzek, K. et al. (1995) Nature 374:378-381).

The cycling of LMW GTP-binding proteins between the GTP-bound active form and the GDP-bound inactive form is regulated by additional proteins. Guanosine nucleotide exchange factors (GEFs) increase the rate of nucleotide dissociation by several orders of magnitude, thus facilitating release of GDP and loading with GTP. Certain Ras-family proteins are also regulated by guanine nucleotide dissociation inhibitors (GDIs), which inhibit GDP dissociation. The intrinsic rate of GTP hydrolysis of the LMW GTP-binding proteins is typically very slow, but it can be stimulated by several orders of magnitude by GTPase-activating proteins (GAPs) (Geyer, M. and Wittinghofer, A. (1997) Curr. Opin. Struct. Biol. 7:786-792).

Heterotrimeric G-proteins are composed of 3 subunits, α, β, and γ, which in their inactive conformation associate as a trimer at the inner face of the plasma membrane. Gα binds GDP or GTP and contains the GTPase activity. The βγ complex enhances binding of Gα to a receptor. Gγ is necessary for the folding and activity of Gβ (Neer, E. J. et al. (1994) Nature 371:297-300). Multiple homologs of each subunit have been identified in mammalian tissues, and different combinations of subunits have specific functions and tissue specificities (Spiegel A. M. (1997) J. Inher. Metab. Dis. 20:113-121). The β subunits, also known as G-β proteins or β transducins, contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. Mutations and variant expression of β transducin proteins are linked with various disorders (Neer, E. J. et al. (1994) Nature 371:297-300; Margottin, F. et al. (1998) Mol. Cell. 1:565-574).

The alpha subunits of heterotrimeric G-proteins can be divided into four distinct classes. The α-s class is sensitive to ADP-ribosylation by pertussis toxin which uncouples the receptor:G-protein interaction. This uncoupling blocks signal transduction to receptors that decrease cAMP levels which normally regulate ion channels and activate phospholipases. The inhibitory α-I class is also susceptible to modification by pertussis toxin which prevents α-I from lowering cAMP levels. Two novel classes of α subunits refractory to pertussis toxin modification are α-q, which activates phospholipase C, and α-12, which has sequence homology with the Drosophila gene concertina and may contribute to the regulation of embryonic development (Simon, M. I. (1991) Science 252:802-808).

The mammalian Gβ and Gγ subunits, each about 340 amino acids long, share more than 80% homology. The Gβ subunit (also called transducin) contains seven repeating units, each about 43 amino acids long. The activity of both subunits may be regulated by other proteins such as calmodulin and phosducin or the neural protein GAP 43 (Clapham, D. and E. Neer (1993) Nature 365:403-406). The β and γ subunits are tightly associated. The β subunit sequences are highly conserved between species, implying that they perform a fundamentally important role in the organization and function of G-protein linked systems (Van der Voorn, L. (1992) FEBS Lett. 307:131-134). They contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. WD-repeat proteins contain from four to eight copies of a loosely conserved repeat of approximately 40 amino acids which participates in protein-protein interactions. Mutations and variant expression of β transducin proteins are linked with various disorders. Mutations in LIS1, a subunit of the human platelet activating factor acetylhydrolase, cause Miller-Dieker lissencephaly. RACK1 binds activated protein kinase C, and RbAp48 binds retinoblastoma protein. CstF is required for polyadenylation of mammalian pre-mRNA in vitro and associates with subunits of cleavage-stimulating factor. Defects in the regulation of β-catenin contribute to the neoplastic transformation of human cells. The WD40 repeats of the human F-box protein bTrCP mediate binding to β-catenin, thus regulating the targeted degradation of β-catenin by ubiquitin ligase (Neer et al., supra; Hart, M. et al. (1999) Curr. Biol 9:207-210). The γ subunit primary structures are more variable than those of the β subunits. They are often post-translationally modified by isoprenylation and carboxyl-methylation of a cysteine residue four amino acids from the C-terminus; this appears to be necessary for the interaction of the βγ subunit with the membrane and with other G-proteins. The βγ subunit has been shown to modulate the activity of isoforms of adenylyl cyclase, phospholipase C, and some ion channels. It is involved in receptor phosphorylation via specific kinases, and has been implicated in the p21ras-dependent activation of the MAP kinase cascade and the recognition of specific receptors by G-proteins (Clapham and Neer, supra).

G-proteins interact with a variety of effectors including adenylyl cyclase (Clapham and Neer, supra). The signaling pathway mediated by cAMP is mitogenic in hormone-dependent endocrine tissues such as adrenal cortex, thyroid, ovary, pituitary, and testes. Cancers in these tissues have been related to a mutationally activated form of a Gα_(s) known as the gsp (Gs protein) oncogene (Dhanasekaran, N. et al. (1998) Oncogene 17:1383-1394). Another effector is phosducin, a retinal phosphoprotein, which forms a specific complex with retinal Gβ and Gγ (Gβγ) and modulates the ability of Gβγ to interact with retinal Gα (Clapham and Neer, supra).

Irregularities in the G-protein signaling cascade may result in abnormal activation of leukocytes and lymphocytes, leading to the tissue damage and destruction seen in many inflammatory and autoimmune diseases such as rheumatoid arthritis, binary cirrhosis, hemolytic anemia, lupus erythematosus, and thyroiditis. Abnormal cell proliferation, including cyclic AMP stimulation of brain, thyroid, adrenal, and gonadal tissue proliferation is regulated by G proteins. Mutations in Gα subunits have been found in growth-hormone-secreting pituitary somatotroph tumors, hyperfunctioning thyroid adenomas, and ovarian and adrenal neoplasms (Meij, J. T. A. (1996) Mol. Cell Biochem. 157:31-38; Aussel, C. et al. (1988) J. Immunol. 140:215-220).

LMW G-proteins are GTPases which regulate cell growth, cell cycle control, protein secretion, and intracellular vesicle interaction. They consist of single polypeptides which, like the alpha subunit of the heterotrimeric G-proteins, are able to bind to and hydrolyze GTP, thus cycling between an inactive and an active state. LMW G-proteins respond to extracellular signals from receptors and activating proteins by transducing mitogenic signals involved in various cell functions. The binding and hydrolysis of GTP regulates the response of LMW G-proteins and acts as an energy source during this process (Bokoch, G. M. and C. J. Der (1993) FASEB J. 7:750-759).

At least sixty members of the 1MW G-protein superfamily have been identified and are currently grouped into the ras, rho, arf, sar1, ran, and rab subfamilies. Activated ras genes were initially found in human cancers, and subsequent studies confirmed that ras function is critical in determining whether cells continue to grow or become differentiated. Ras1 and Ras2 proteins stimulate adenylate cyclase (Kaziro et al., supra), affecting a broad array of cellular processes. Stimulation of cell surface receptors activates Ras which, in turn, activates cytoplasmic kinases. These kinases translocate to the nucleus and activate key transcription factors that control gene expression and protein synthesis (Barbacid, M. (1987) Annu. Rev. Biochem. 56:779-827; Treisman, R (1994) Curr. Opi Genet. Dev. 4:96-98). Other members of the 1MW G-protein superfamily have roles in signal transduction that vary with the function of the activated genes and the locations of the G-proteins that initiate the activity. Rho G-proteins control signal transduction pathways that link growth factor receptors to actin polymerization, which is necessary for normal cellular growth and division. The rab, arf, and sar1 families of proteins control the translocation of vesicles to and from membranes for protein processing, localization, and secretion. Vesicle- and target-specific identifiers (v-SNAREs and t-SNAREs) bind to each other and dock the vesicle to the acceptor membrane. The budding process is regulated by the closely related ADP ribosylation factors (ARFs) and SAR proteins, while rab proteins allow assembly of SNARE complexes and may play a role in removal of defective complexes (Rothman, J. and F. Wieland (1996) Science 272:227-234). Ran G-proteins are located in the nucleus of cells and have a key role in nuclear protein import, the control of DNA synthesis, and cell-cycle progression (Hall, A. (1990) Science 249:635-640; Barbacid, supra; Ktistakis, N. (1998) BioEssays 20:495-504; and Sasaki, T. and Y. Takai (1998) Biochem. Biophys. Res. Commun. 245:641-645).

The function of Rab proteins in vesicular transport requires the cooperation of many other proteins. Specifically, the membrane-targeting process is assisted by a series of escort proteins (Khosravi-Far, R. et al. (1991) Proc. Natl. Acad. Sci. USA 88:6264-6268). In the medial Golgi, it has been shown that GTP-bound Rab proteins initiate the binding of VAMP-like proteins of the transport vesicle to syntaxin-like proteins on the acceptor membrane, which subsequently triggers a cascade of protein-binding and membrane-fusion events. After transport, GTPase-activating proteins (GAPs) in the target membrane are responsible for converting the GTP-bound Rab proteins to their GDP-bound state. And finally, guanine-nucleotide dissociation inhibitor (GDI) recruits the GDP-bound proteins to their membrane of origin.

The cycling of LMW G-proteins between the GTP-bound active form and the GDP-bound inactive form is regulated by a variety of proteins. Guanosine nucleotide exchange factors (GEFs) increase the rate of nucleotide dissociation by several orders of magnitude, thus facilitating release of GDP and loading with GTP. The best characterized is the mammalian homolog of the Drosophila Son-of-Sevenless protein. Certain Ras-family proteins are also regulated by guanine nucleotide dissociation inhibitors (GDIs), which inhibit GDP dissociation The intrinsic rate of GTP hydrolysis of the LMW G-proteins is typically very slow, but it can be stimulated by several orders of magnitude by GTPase-activating proteins (GAPs) (Geyer, M. and A. Wittinghofer (1997) Curr. Opin. Struct. Biol 7:786-792). Both GEF and GAP activity may be controlled in response to extracellular stimuli and modulated by accessory proteins such as RalBP1 and POB1. Mutant Ras-family proteins, which bind but cannot hydrolyze GTP, are permanently activated, and cause cell proliferation or cancer, as do GEFs that inappropriately activate LMW G-proteins, such as the human oncogene NET1, a Rho-GEF (Drivas, G. T. et al. (1990) Mol. Cell Biol. 10:1793-1798; Alberts, A. S. and P Treisman (1998) EMBO J. 14:4075-4085).

A member of the ARM family of G-proteins is centaurin beta 1A, a regulator of membrane traffic and the actin cytoskeleton. The centaurin β family of GTPase-activating proteins (GAPs) and Arf guanine nucleotide exchange factors contain pleckstrin homology (PH) domains which are activated by phosphoinositides. PH domains bind phosphoinositides, implicating PH domains in signaling processes. Phosphoinositides have a role in converting Arf-GTP to Arf-GDP via the centaurin β family and a role in Arf activation (Kam, J. L. et al. (2000) J. Biol. Chem. 275:9653-9663). The rho GAP family is also implicated in the regulation of actin polymerization at the plasma membrane and in several cellular processes. The gene ARHGAP6 encodes GTPase-activating protein 6 isoform 4. Mutations in ARHGAP6, seen as a deletion of a 500 kb critical region in Xp22.3, causes the syndrome microphthalmia with linear skin defects (MLS). MLS is an X-linked dominant, male-lethal syndrome (Prakash, S. K. et al. (2000) Hum. Mol. Genet. 9:477-488).

Rab proteins have a highly variable amino terminus containing membrane-specific signal information and a prenylated carboxy terminus which determines the target membrane to which the Rab proteins anchor. More than 30 Rab proteins have been identified in a variety of species, and each has a characteristic intracellular location and distinct transport function. In particular, Rab1 and Rab2 are important in ER-to-Golgi transport; Rab3 transports secretory vesicles to the extracellular membrane; Rab5 is localized to endosomes and regulates the fusion of early endosomes into late endosomes; Rab6 is specific to the Golgi apparatus and regulates intra-Golgi transport events; Rab7 and Rab9 stimulate the fusion of late endosomes and Golgi vesicles with lysosomes, respectively; and Rab10 mediates vesicle fusion from the medial Golgi to the trans Golgi. Mutant forms of Rab proteins are able to block protein transport along a given pathway or alter the sizes of entire organelles. Therefore, Rabs play key regulatory roles in membrane trafficking (Schimmöler, I. S. and S. R. Pfeffer (1998) J. Biol. Chem. 243:22161-22164).

The function of Rab proteins in vesicular transport requires the cooperation of many other proteins. Specifically, the membrane-targeting process is assisted by a series of escort proteins (Khosravi-Far, R et al. (1991) Proc. Natl Acad. Sci. USA 88:6264-6268). In the medial Golgi, it has been shown that GTP-bound Rab proteins initiate the binding of VAMP-like proteins of the transport vesicle to syntaxin-like proteins on the acceptor membrane, which subsequently triggers a cascade of protein-binding and membrane-fusion events. After transport, GTPase-activating proteins (GAPs) in the target membrane are responsible for converting the GTP-bound Rab proteins to their GDP-bound state. Finally, guanine-nucleotide dissociation inhibitor (GDI) recruites the GDP-bound proteins to their membrane of origin.

Other regulators of G-protein signaling (RGS) also exist that act primarily by negatively regulating the G-protein pathway by an unknown mechanism (Druey, K. M. et al (1996) Nature 379:742-746). Some 15 members of the RGS family have been identified. RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their ability to inhibit the interleukin (cytokine) induction of MAP kinase in cultured mammalian 293T cells (Druey et al., supra).

A member of the Rho family of G-proteins is CDC42, a regulator of cytoskeletal rearrangements required for cell division. CDC42 is inactivated by a specific GAP (CDC42GAP) that strongly stimulates the GTPase activity of CDC42 while having a much lesser effect on other Rho family members. CDC42GAP also contains an SH3-binding domain that interacts with the SH3 domains of cell signaling proteins such as p85 alpha and c-Src, suggesting that CDC42GAP may serve as a link between CDC42 and other cell signaling pathways (Barfod, E. T. et al. (1993) J. Biol. Chem. 268:26059-26062).

The Dbl proteins are a family of GEFs for the Rho and Ras G-proteins (Whitehead, I. P. et al. (1997) Biochim. Biophys. Acta 1332:F1-F23). All Dbl family members contain a Dbl homology (DH) domain of approximately 180 amino acids, as well as a pleckstrin homology (PH) domain located immediately C-terminal to the DH domain. Most Dbl proteins have oncogenic activity, as demonstrated by the ability to transform various cell lines, consistent with roles as regulators of Rho-mediated oncogenic signaling pathways. The kalirin proteins are neuron-specific members of the Dbl family, which are located to distinct subcellular regions of cultured neurons (Johnson, R. C. (2000) J. Cell Biol. 275:19324-19333).

Other regulators of G-protein signaling (RGS) also exist that act primarily by negatively regulating the G-protein pathway by an unknown mechanism (Druey, K. M. et al. (1996) Nature 379:742-746). Some 15 members of the RGS family have been identified. RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their ability to inhibit the interleukin (cytokine) induction of MAP kinase in cultured mammalian 293T cells (Druey et al., supra).

The Immuno-associated nucleotide (IAN) family of proteins has GTP-binding activity as indicated by the conserved ATP/GTP-binding site P-loop motif. The IAN family includes IAN-1, IAN-4, IAP38, and IAG-1. IAN-1 is expressed in the immune system, specifically in T cells and thymocytes. Its expression is induced during thymic events (Poirier, G. M. C. et al. (1999) J. Immunol. 163:4960-4969). IAP38 is expressed in B cells and macrophages and its expression is induced in splenocytes by pathogens. IAG-1, which is a plant molecule, is induced upon bacterial infection (Krucken, J. et al. (1997) Biochem. Biophys. Res. Commun 230:167-170). IAN-4 is a mitochondrial membrane protein which is preferentially expressed in hematopoietic precursor 32D cells transfected with wild-type versus mutant forms of the bcr/abl oncogene. The bcr/abl oncogene is known to be associated with chronic myelogenous leukemia, a clonal myelo-proliferative disorder, which is due to the translocation between the bcr gene on chromosome 22 and the abl gene on chromosome 9. Bcr is the breakpoint cluster region gene and abl is the cellular homolog of the transforming gene of the Abelson murine leukemia virus. Therefore, the IAN family of proteins appears to play a role in cell survival in immune responses and cellular transformation (Daheron, L. et al. (2001) Nucleic Acids Res. 29:1308-1316).

Formin-related genes (FRL) comprise a large family of morphoregulatory genes and have been shown to play important roles in morphogenesis, embryogenesis, cell polarity, cell migration, and cytokinesis through their interaction with Rho family small GTPases. Formin was first identified in mouse limb deformity (ld) mutants where the distal bones and digits of all limbs are fused and reduced in size. FRL contains formin homology domains FH1, FH2, and FEB. The FH1 domain has been shown to bind the Src homology 3 (SH3) domain, WWP/WW domains, and profilin. The FH2 domain is conserved and was shown to be essential for formin function as disruption at the FM2 domain results in the characteristic ld phenotype. The FIB domain is located at the N-terminus of FRL, and is required for associating with Rac, a Rho family GTPase (Yayoshi-Yamamoto, S. et al. (2000) Mol. Cell. Biol. 20:6872-6881).

Signaling Complex Protein Domains

PDZ domains were named for three proteins in which this domain was initially discovered. These proteins include PSD-95 (postsynaptic density 95), Dlg (Drosophila lethal(1)discs large-1), and ZO-1 (zonula occludens-1). These proteins play important roles in neuronal synaptic transmission, tumor suppression, and cell junction formation, respectively. Since the discovery of these proteins, over sixty additional PDZ-containing proteins have been identified in diverse prokaryotic and eukaryotic organisms. This domain has been implicated in receptor and ion channel clustering and in the targeting of multiprotein signaling complexes to specialized functional regions of the cytosolic face of the plasma membrane. (or a review of PDZ domain-containing proteins, see Ponting, C. P. et al (1997) Bioessays 19:469-479.) A large proportion of PDZ domains are found in the eukaryotic MAGUK (membrane-associated guanylate kinase) protein family, members of which bind to the intracellular domains of receptors and channels. However, PDZ domains are also found in diverse membrane-localized proteins such as protein tyrosine phosphatases, serine/threonine kinases, G-protein cofactors, and synapse-associated proteins such as syntrophins and neuronal nitric oxide synthase (nNOS). Generally, about one to three PDZ domains are found in a given protein, although up to nine PDZ domains have been identified in a single protein The glutamate receptor interacting protein (GRIP) contains seven PDZ domains. GRIP is an adaptor that links certain glutamate receptors to other proteins and may be responsible for the clustering of these receptors at excitatory synapses in the brain (Dong, H. et al. (1997) Nature 386:279-284). The Drosophila scribble (SCRIB) protein contains both multiple PDZ domains and leucine-rich repeats. SCRIB is located at the epithelial septate junction, which is analogous to the vertebrate tight junction, at the boundary of the apical and basolateral cell surface. SCRIB is involved in the distribution of apical proteins and correct placement of adherens junctions to the basolateral cell surface (Bilder, D. and N. Perrimon (2000) Nature 403:676-680).

The PX domain is an example of a domain specialized for promoting protein-protein interactions. The PX domain is found in sorting nexins and in a variety of other proteins, including the PhoX components of NADPH oxidase and the Cpk class of phosphatidylinositol 3-kinase. Most PX domains contain a polyproline motif which is characteristic of SH3 domain-binding proteins (Ponting, C. P. (1996) Protein Sci. 5:2353-2357). SI3 domain-mediated interactions involving the PhoX components of NADPH oxidase play a role in the formation of the NADPH oxidase multi-protein complex (Leto, T. L. et al. (1994) Proc. Natl. Acad. Sci. USA 91:10650-10654; Wilson, L. et al. (1997) Inflamm. Res. 46:265-271).

The SH3 domain is defined by homology to a region of the proto-oncogene c-Src, a cytoplasmic protein tyrosine kinase. SH3 is a small domain of 50 to 60 amino acids that interacts with proline-rich ligands. SH3 domains are found in a variety of eukaryotic proteins involved in signal transduction, cell polarization, and membrane-cytoskeleton interactions. In some cases, SH3 domain-containing proteins interact directly with receptor tyrosine kinases. For example, the SLAP-130 protein is a substrate of the T-cell receptor (TCR) stimulated protein kinase. SLAP-130 interacts via its SH3 domain with the protein SLP-76 to affect the TCR-induced expression of interleukin-2 (Musci, M. A. et al. (1997) J. Biol. Chem. 272:11674-11677). Another recently identified SH3 domain protein is macrophage actin-associated tyrosine-phosphorylated protein (MAYP) which is phosphorylated during the response of macrophages to colony stimulating factor-1 (CSF-1) and is likely to play a role in regulating the CSF-1-induced reorganization of the actin cytoskeleton (Yeung, Y.-G. et al. (1998) J. Biol. Chem. 273:30638-30642). The structure of the SH3 domain is characterized by two antiparallel beta sheets packed against each other at right angles. This packing forms a hydrophobic pocket lined with residues that are highly conserved between different 53 domains. This pocket makes critical hydrophobic contacts with proline residues in the ligand (Feng, S. et al. (1994) Science 266:1241-1247).

A novel domain, called the WW domain, resembles the SH3 domain in its ability to bind proline-rich ligands. This domain was originally discovered in dystrophin, a cytoskeletal protein with direct involvement in Duchenne muscular dystrophy (Bork, P. and M. Sudol (1994) Trends Biochem. Sci. 19:531-533). WW domains have since been discovered in a variety of intracellular signaling molecules involved in development, cell differentiation, and cell proliferation. The structure of the WW domain is composed of beta strands grouped around four conserved aromatic residues, generally tryptophan.

Lie SH3, the SH2 domain is defined by homology to a region of c-Src. SH2 domains interact directly with phospho-tyrosine residues, thus providing an immediate mechanism for the regulation and transduction of receptor tyrosine kinase-mediated signaling pathways. For example, as many as ten distinct SH2 domains are capable of binding to phosphorylated tyrosine residues in the activated PDGF receptor, thereby providing a highly coordinated and finely tuned response to ligand-mediated receptor activation. (Reviewed in Schaffhausen, B. (1995) Biochim Biophys. Acta. 1242:61-75.) The BLNK protein is a linker protein involved in B cell activation, that bridges B cell receptor-associated kinases with SH2 domain effectors that link to various signaling pathways (Fu, C. et al. (1998) Immunity 9:93-103).

The pleckstrin homology PH) domain was originally identified in pleckstrin, the predominant substrate for protein kinase C in platelets. Since its discovery, this domain has been identified in over 90 proteins involved in intracellular signaling or cytoskeletal organization. Proteins containing the pleckstrin homology domain include a variety of kinases, phospholipase-C isoforms, guanine nucleotide release factors, and GTPase activating proteins. For example, members of the FGD1 family contain both Rho-guanine nucleotide exchange factor (GEF) and PH domains, as well as a FYVE zinc finger domain. FGD1 is the gene responsible for faciogenital dysplasia, an inherited skeletal dysplasia (Pasteris, N. G. and J. L. Gorski (1999) Genomics 60:57-66). Many PH domain proteins function in association with the plasma membrane, and this association appears to be mediated by the PH domain itself. PH domains share a common structure composed of two antiparallel beta sheets flanked by an amphipathic alpha helix. Variable loops connecting the component beta strands generally occur within a positively charged environment and may function as ligand binding sites (Lemmon, M. A. et al. (1996) Cell 85:621-624). Ankrin (ANK) repeats mediate protein-protein interactions associated with diverse intracellular signaling functions. For example, ANK repeats are found in proteins involved in cell proliferation such as kinases, kinase inhibitors, tumor suppressors, and cell cycle control proteins. (See, for example, Kalus, W. et al (1997) FEBS Lett. 401:127-132; Ferrante, A. W. et al. (1995) Proc. Natl. Acad. Sci. USA 92:1911-1915.) These proteins generally contain multiple ANK repeats, each composed of about 33 amino acids. Myotrophin is an ANK repeat protein that plays a key role in the development of cardiac hypertrophy, a contributing factor to many heart diseases. Structural studies show that the myotrophin ANK repeats, like other ANK repeats, each form a helix-turn-helix core preceded by a protruding “tip.” These tips are of variable sequence and may play a role in protein-protein interactions. The helix-turn-helix region of the ANK repeats stack on top of one another and are stabilized by hydrophobic interactions (Yang, Y. et al. (1998) Structure 6:619-626). Members of the ASB protein family contain a suppressor of cytokine signaling (SOCS) domain as well as multiple ankyrin repeats (Hilton, D. J. et al. (1998) Proc. Natl. Acad. Sci. USA 95:114-119).

The tetratricopeptide repeat (TPR) is a 34 amino acid repeated motif found in organisms from bacteria to humans. TPRs are predicted to form ampipathic helices, and appear to mediate protein-protein interactions. TPR domains are found in CDC16, CDC23, and CDC27, members of the anaphase promoting complex which targets proteins for degradation at the onset of anaphase. Other processes involving TPR proteins include cell cycle control, transcription repression, stress response, and protein kinase inhibition (Lamb, J. R. et al. (1995) Trends Biochem. Sci. 20:257-259).

The armadillo/beta-catenin repeat is a 42 amino acid motif which forms a superhelix of alpha helices when tandemly repeated. The structure of the armadillo repeat region from beta-catenin revealed a shallow groove of positive charge on one face of the superhelix, which is a potential binding surface. The armadillo repeats of beta-catenin, plakoglobin, and p120^(cas) bind the cytoplasmic domains of cadherins. Betaatenin/cadherin complexes are targets of regulatory signals that govern cell adhesion and mobility (Huber, A. H. et al. (1997) Cell 90:871-882).

Eight tandem repeats of about 40 residues (WD-40 repeats), each containing a central Trp-Asp motif, make up beta-transducin (G-beta), which is one of the three subunits (alpha, beta, and gamma) of the guanine nucleotide-binding proteins (G proteins). In higher eukaryotes G-beta exists as a small multigene family of highly conserved proteins of about 340 amino acid residues. WD repeats are also found in other protein families. For example, betaTRCP is a component of the ubiquitin ligase complex, which recruits specific proteins, including beta-catenin, to the ubiquitin-proteasome degradation pathway. BetaTRCP and its isoforms all contain seven WD repeats, as well as a characteristic “F-box” motif. (Koike, J. et al (2000) Biochem. Biophys. Res. Commun. 269:103-109.)

Signaling by Notch family receptors controls cell fate decisions during development (Frisen, J. and Lendabl, U. (2001) Bioessays 23:3-7). The Notch receptor signing pathway is involved in the morphogenesis and development of many organs and tissues in multicellular species. Notch receptors are large transmembrane proteins that contain extracellular regions made up of repeated EGF domains. Notchless was identified in a screen for molecules that modulate notch activity (Royet, J. et al. (1998) EMBO J. 17:7351-7360). Notchless, which contains nine WD40 repeats, binds to the cytoplasmic domain of Notch and inhibits Notch activity. Eps8 is a substrate for the intracellular epidermal growth factor receptors (EGR).

Semaphorins are secreted, glycosylphosphatidylinositol (GPI) anchor and transmembrane glycoproteins. Semaphorins function as chemorepellants in various sensory and motor axons (Soker, S. (2001) Int. 3. Biochem. Cell Biol. 33:433437). Semaphorins constitute one type of ligand for the plexin receptor.

Tumor necrosis factor receptor-associated factors (TRAFs) constitute a family of adaptor proteins that link the cytosolic domains of these receptors to downstream protein kinases or WD repeats are also found in other protein families. For example, betaTRCP is a component of the ubiquitin ligases. These proteins share a TRAP domain (TD), a distinctive region near the COOH terminus, that is responsible for mediating interactions between TRAFs and TNF receptors with other adaptor proteins and kinases.

Expression Profiling

Microarrays are analytical tools used in bioanalysis. A microarray has a plurality of molecules spatially distributed over, and stably associated with, the surface of a solid support. Microarrays of polypeptides, polynucleotides, and/or antibodies have been developed and find use in a variety of applications, such as gene sequencing, monitoring gene expression, gene mapping, bacterial identification, drug discovery, and combinatorial chemistry.

One area in particular in which microarrays find use is in gene expression analysis. Array technology can provide a simple way to explore the expression of a single polymorphic gene or the expression profile of a large number of related or unrelated genes. When the expression of a single gene is examined, arrays are employed to detect the expression of a specific gene or its variants. When an expression profile is examined, arrays provide a platform for identifying genes that are tissue specific, are affected by a substance being tested in a toxicology assay, are part of a signaling cascade, carry out housekeeping functions, or are specifically related to a particular genetic predisposition, condition, disease, or disorder.

Steroid Hormones

Steroids are a class of lipid-soluble molecules, including cholesterol bile acids, vitamin D, and hormones, that share a common four-ring structure based on cyclopentanoperhydrophenanthrene and that carry out a wide variety of functions. Cholesterol, for example, is a component of cell membranes that controls membrane fluidity. It is also a precursor for bile acids which solubilize lipids and facilitate absorption in the small intestine during digestion. Vitamin D regulates the absorption of calcium in the small intestine and controls the concentration of calcium in plasma. Steroid hormones, produced by the adrenal cortex, ovaries, and testes, include glucocorticoids, mineralocorticoids, androgens, and estrogens. They control various biological processes by binding to intracellular receptors that regulate transcription of specific genes in the nucleus. Glucocorticoids, for example, increase blood glucose concentrations by regulation of gluconeogenesis in the liver, increase blood concentrations of fatty acids by promoting lipolysis in adipose tissues, modulate sensitivity to catcholamines in the central nervous system, and reduce inflammation. The principal mineralocorticoid, aldosterone, is produced by the adrenal cortex and acts on cells of the distal tubules of the kidney to enhance sodium ion reabsorption. Androgens, produced by the interstitial cells of Leydig in the testis, include the male sex hormone testosterone, which triggers changes at puberty, the production of sperm and maintenance of secondary sexual characteristics. Female sex hormones, estrogen and progesterone, are produced by the ovaries and also by the placenta and adrenal cortex of the fetus during pregnancy. Estrogen regulates female reproductive processes and secondary sexual characteristics. Progesterone regulates changes in the endometrium during the menstrual cycle and pregnancy.

Steroid hormones are widely used for fertility control and in anti-inflammatory treatments for physical injuries and diseases such as arthritis, asthma, and auto-immune disorders. Progesterone, a naturally occurring progestin, is primarily used to treat amenorrhea, abnormal uterine bleeding, or as a contraceptive. Endogenous progesterone is responsible for inducing secretory activity in the endometrium of the estrogen-primed uterus in preparation for the implantation of a fertilized egg and for the maintenance of pregnancy. It is secreted from the corpus luteum in response to luteinizing hormone (LH). The primary contraceptive effect of exogenous progestins involves the suppression of the midcycle surge of LH. At the cellular level progestins diffuse freely into target cells and bind to the progesterone receptor. Target cells include the female reproductive tract, the mammary gland, the hypothalamus, and the pituitary. Once bound to the receptor, progestins slow the frequency of release of gonadotropin releasing hormone from the hypothalamus and blunt the pre-ovulatory LH surge, thereby preventing follicular maturation and ovulation Progesterone has minimal estrogenic and androgenic activity. Progesterone is metabolized hepatically to pregnanediol and conjugated with glucuronic acid.

Medroxyprogesterone (MAH), also known as 6α-methyl-17-hydroxyprogesterone, is a synthetic progestin with a pharmacological activity about 15 times greater than progesterone. MAH is used for the treatment of renal and endometrial carcinomas, amenorrhea, abnormal uterine bleeding, and endometriosis associated with hormonal imbalance. MAH has a stimulatory effect on respiratory centers and has been used in cases of low blood oxygenation caused by sleep apnea, chronic obstructive pulmonary disease, or hypercapnia.

Mifepristone, also known as RU-486, is an antiprogesterone drug that blocks receptors of progesterone. It counteracts the effects of progesterone, which is needed to sustain pregnancy. Mifepristone induces spontaneous abortion when administered in early pregnancy followed by treatment with the prostaglandin, misoprostol. Further, studies show that mifepristone at a substantially lower dose can be highly effective as a postcoital contraceptive when administered within five days after unprotected intercourse, thus providing women with a “morning-after pill” in case of contraceptive failure or sexual assault. Mifepristone also has potential uses in the treatment of breast and ovarian cancers in cases in which tumors are progesterone-dependent. It interferes with steroid-dependent growth of brain meningiomas, and may be useful in treatment of endometriosis where it blocks the estrogen-dependent growth of endometrial tissues. It may also be useful in treatment of uterine fibroid tumors and Cushing's Syndrome. Mifepristone binds to glucocorticoid receptors and interferes with cortisol binding. Mifepristone also may act as an anti-glucocorticoid and be effective for treating conditions where cortisol levels are elevated such as AIDS, anorexia nervosa, ulcers, diabetes, Parkinson's disease, multiple sclerosis, and Alzheimer's disease.

Danazol is a synthetic steroid derived from ethinyl testosterone. Danazol indirectly reduces estrogen production by lowering pituitary synthesis of follicle-stimulating hormone and LH. Danazol also binds to sex hormone receptors in target tissues, thereby exhibting anabolic, antiestrognic, and weakly androgenic activity. Danazol does not possess any progestogenic activity, and does not suppress normal pituitary release of corticotropin or release of cortisol by the adrenal glands. Danazol is used in the treatment of endometriosis to relieve pain and inhibit endometrial cell growth. It is also used to treat fibrocystic breast disease and hereditary angioedema.

Corticosteroids are used to relieve inflammation and to suppress the immune response. They inhibit eosinophil, basophil, and airway epithelial cell function by regulation of cytolines that mediate the inflammatory response. They inhibit leukocyte infiltration at the site of inflammation, interfere in the function of mediators of the inflammatory response, and suppress the humoral immune response. Corticosteroids are used to treat allergies, asthma, arthritis, and skin conditions. Beclomethasone is a synthetic glucocorticoid that is used to treat steroid-dependent asthma, to relieve symptoms associated with allergic or nonallergic (vasomotor) rhinitis, or to prevent recurrent nasal polyps following surgical removal The anti-inflammatory and vasoconstrictive effects of intranasal beclomethasone are 5000 times greater than those produced by hydrocortisone. Budesonide is a corticosteroid used to control symptoms associated with allergic rhinitis or asthma Budesonide has high topical anti-inflammatory activity but low systemic activity. Dexamethasone is a synthetic glucocorticoid used in anti-inflammatory or immunosuppressive compositions. It is also used in inhalants to prevent symptoms of asthma. Due to its greater ability to reach the central nervous system, dexamethasone is usually the treatment of choice to control cerebral edema. Dexamethasone is approximately 20-30 times more potent than hydrocortisone and 5-7 times more potent than prednisone. Prednisone is metabolized in the liver to its active form, prednisolone, a glucocorticoid with anti-inflammatory properties. Prednisone is approximately 4 times more potent than hydrocortisone and the duration of action of prednisone is intermediate between hydrocortisone and dexamethasone. Prednisone is used to treat allograft rejection, asthma, systemic lupus eryihematosus, arthritis, ulcerative colitis, and other inflammatory conditions. Betamethasone is a synthetic glucocorticoid with antiinflammatory and immunosuppressive activity and is used to treat psoriasis and fungal infections, such as athlete's foot and ringworm.

The anti-inflammatory actions of corticosteroids are thought to involve phospholipase A₂ inhibitory proteins, collectively called lipocortins. Lipocortins, in turn, control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of the precursor molecule arachidonic acid. Proposed mechanisms of action include decreased IgE synthesis, increased number of β-adrenergic receptors on leukocytes, and decreased arachidonic acid metabolism. During an immediate allergic reaction, such as in chronic bronchial asthma, allergens bridge the IgE antibodies on the surface of mast cells, which triggers these cells to release chemotactic substances. Mast cell influx and activation, therefore, is partially responsible for the inflammation and hyperirritability of the oral mucosa in asthmatic patients. This inflammation can be retarded by administration of corticosteroids.

Immune Response Cells and Proteins

Human peripheral blood mononuclear cells (PBMCs) contain B lymphocytes, T lymphocytes, NK cells, monocytes, dendritic cells and progenitor cells.

Glucocorticoids are naturally occurring hormones that prevent or suppress inflammation and immune responses when administered at pharmacological doses. Unbound glucocorticoids readily cross cell membranes and bind with high affinity to specific cytoplasmic receptors. Subsequent to binding, transcription and protein synthesis are affected. The result can include inhibition of leukocyte infiltration at the site of inflammation, interference in the function of mediators of inflammatory response, and suppression of humoral immune responses. The anti-inflammatory actions of corticosteroids are thought to involve phospholipase A2 inhibitory proteins, collectively called lipocortins. Lipocortins, in turn, control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of the precursor arachidonic molecule.

Staphylococcal exotoxins specifically activate human T cells, expressing an appropriate TCR-Vbeta chain. Although polyclonal in nature, T cells activated by Staphylococcal exotoxins require antigen presenting cells (APCs) to present the exotoxin molecules to the T cells and deliver the costimulatory signals required for optimum T cell activation. Although Staphylococcal exotoxins must be presented to T cells by APCs, these molecules need not be processed by APC. Staphylococcal exotoxins directly bind to a non-polymorphic portion of the human MHC class II molecules, bypassing the need for capture, cleavage, and binding of the peptides to the polymorphic antigenic groove of the MHC class II molecules.

Colon Cancer

The potential application of gene expression profiling is particularly relevant to improving diagnosis, prognosis, and treatment of cancers, such as colon cancer. Colon cancer evolves through a multi-step process whereby pre-malignant colonocytes undergo a relatively defined sequence of events leading to tumor formation. Several factors participate in the process of tumor progression and malignant transformation including genetic factors, mutations, and selection.

To understand the nature of gene alterations in colorectal cancer, a number of studies have focused on the inherited syndromes. Familial adenomatous polyposis (FAP), is caused by mutations in the adenomatous polyposis coli gene (APC), resulting in truncated or inactive forms of the protein. This tumor suppressor gene has been mapped to chromosome 5q. Hereditary nonpolyposis colorectal cancer (HNPCC) is caused by mutations in mis-match repair genes. Although hereditary colon cancer syndromes occur in a small percentage of the population and most colorectal cancers are considered sporadic, knowledge from studies of the hereditary syndromes can be generally applied. For instance, somatic mutations in APC occur in at least 80% of sporadic colon tumors. APC mutations are thought to be the initiating event in the disease. Other mutations occur subsequently. Approximately 50% of colorectal cancers contain activating mutations in ras, while 85% contain inactivating mutations in p53. Changes in all of these genes lead to gene expression changes in colon cancer.

There is a need in the art for new compositions, including nucleic acids and proteins, for the diagnosis, prevention, and treatment of cell proliferative, endocrine, autoimmune/inflammatory, neurological, gastrointestinal, reproductive, developmental, and vesicle trafficking disorders.

SUMMARY OF THE INVENTION

Various embodiments of the invention provide purified polypeptides, intracellular signaling molecules, referred to collectively as ‘INTSIG’ and individually as ‘INTSIG-1,’ ‘INTSIG-2,’ ‘INTSIG-3,’ ‘INTSIG4,’ ‘INTSIG-5,’ ‘INTSIG-6,’ ‘INTSIG-7,’ ‘INTSIG-8,’ ‘INTSIG-9,’ ‘INTSIG-10,’ ‘INTSIG-11,’ ‘INTSIG-12,’ ‘INTSIG-13,’ ‘INTSIG-14,’ ‘INTSIG-15,’ ‘INTSIG-16,’ ‘INTSIG-17,’ ‘INTSIG-18,’ ‘INTSIG-19,’ ‘INTSIG-20,’ ‘INTSIG-21,’ ‘INTSIG-22,’ ‘INTSIG-23,’ ‘INTSIG-24,’ ‘INTSIG-25,’ ‘INTSIG-26,’ ‘INTSIG-27,’ ‘INTSIG-28,’ ‘INTSIG-29,’ ‘INTSIG-30,’ ‘INTSIG-31,’ ‘INTSIG-32,’ ‘INTSIG-33,’ ‘INTSIG-34,’ ‘INTSIG-35,’ ‘INTSIG-36,’ ‘INTSIG-37,’ ‘INTSIG-38,’ ‘INTSIG-39,’ ‘INTSIG-40,’ ‘INTSIG-41,’ ‘INTSIG-42,’ ‘INTSIG-43,’ INTSIG-44,’ and ‘INTSIG-45’ and methods for using these proteins and their encoding polynucleotides for the detection, diagnosis, and treatment of diseases and medical conditions. Embodiments also provide methods for utilizing the purified intracellular signaling molecules and/or their encoding polynucleotides for facilitating the drug discovery process, including determination of efficacy, dosage, toxicity, and pharmacology. Related embodiments provide methods for utilizing the purified intracellular signaling molecules and/or their encoding polynucleotides for investigating the pathogenesis of diseases and medical conditions.

An embodiment provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. Another embodiment provides an isolated polypeptide comprising an amino acid sequence of SEQ ID NO:1-45.

Still another embodiment provides an isolated polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:145, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. In another embodiment, the polynucleotide encodes a polypeptide selected from the group consisting of SEQ ID NO:1-45. In an alternative embodiment, the polynucleotide is selected from the group consisting of SEQ ID NO:46-90.

Still another embodiment provides a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ED NO:1-45. Another embodiment provides a cell transformed with the recombinant polynucleotide. Yet another embodiment provides a transgenic organism comprising the recombinant polynucleotide.

Another embodiment provides a method for producing a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. The method comprises a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding the polypeptide, and b) recovering the polypeptide so expressed.

Yet another embodiment provides an isolated antibody which specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45.

Still yet another embodiment provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). In other embodiments, the polynucleotide can comprise at least about 20, 30, 40, 60, 80, or 100 contiguous nucleotides.

Yet another embodiment provides a method for detecting a target polynucleotide in a sample, said target polynucleotide being selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex. In a related embodiment, the method can include detecting the amount of the hybridization complex In still other embodiments, the probe can comprise at least about 20, 30, 40, 60, 80, or 100 contiguous nucleotides.

Still yet another embodiment provides a method for detecting a target polynucleotide in a sample, said target polynucleotide being selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). The method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof. In a related embodiment the method can include detecting the amount of the amplified target polynucleotide or fragment thereof.

Another embodiment provides a composition comprising an effective amount of a polypeptide elected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and a pharmaceutically acceptable excipient. In one embodiment, the composition can comprise an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. Other embodiments provide a method of treating a disease or condition associated with decreased or abnormal expression of functional INTSIG, comprising administering to a patient in need of such treatment the composition Yet another embodiment provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting agonist activity in the sample. Another embodiment provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient. Yet another embodiment provides a method of treating a disease or condition associated with decreased expression of functional INTSIG, comprising administering to a patient in need of such treatment the composition.

Still yet another embodiment provides a method for screening a compound for effectiveness as an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting antagonist activity in the sample. Another embodiment provides a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient. Yet another embodiment provides a method of treating a disease or condition associated with overexpression of functional INTSIG, comprising administering to a patient in need of such treatment the composition.

Another embodiment provides a method of screening for a compound that specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. The method comprises a) combining the polypeptide with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide to the test compound, thereby identifying a compound that specifically binds to the polypeptide.

Yet another embodiment provides a method of screening for a compound that modulates the activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45. The method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.

Still yet another embodiment provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, the method comprising a) exposing a sample comprising the target polynucleotide to a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

Another embodiment provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, iii) a polynucleotide having a sequence complementary to i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i)-iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, iii) a polynucleotide complementary to the polynucleotide of i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i)-iv). Alternatively, the target polynucleotide can comprise a fragment of a polynucleotide selected from the group consisting of i)-v) above; c) quantifying the amount of hybridization complex; and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

BRIEF DESCRIPTION OF THE TABLES

Table 1 summarizes the nomenclature for fall length polynucleotide and polypeptide embodiments of the invention.

Table 2 shows the GenBank identification number and annotation of the nearest GenBank homolog, and the PROTEOME database identification numbers and annotations of PROTEOME database homologs, for polypeptide embodiments of the invention. The probability scores for the matches between each polypeptide and its homolog(s) are also shown.

Table 3 shows structural features of polypeptide embodiments, including predicted motifs and domains, along with the methods, algorithms, and searchable databases used for analysis of the polypeptides.

Table 4 lists the cDNA and/or genomic DNA fragments which were used to assemble polynucleotide embodiments, along with selected fragments of the polynucleotides.

Table 5 shows representative cDNA libraries for polynucleotide embodiments.

Table 6 provides an appendix which describes the tissues and vectors used for construction of the cDNA libraries shown in Table 5.

Table 7 shows the tools, programs, and algorithms used to analyze polynucleotides and polypeptides, along with applicable descriptions, references, and threshold parameters.

Table 8 shows single nucleotide polymorphisms found in polynucleotide sequences of the invention, along with allele frequencies in different human populations.

DESCRIPTION OF THE INVENTION

Before the present proteins, nucleic acids, and methods are described, it is understood that embodiments of the invention are not limited to the particular machines, instruments, materials, and methods described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the invention.

As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “an antibody” is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any machines, materials, and methods similar or equivalent to those described herein can be used to practice or test the present invention, the preferred machines, materials and methods are now described. All publications mentioned herein are cited for the purpose of describing and disclosing the cell lines, protocols, reagents and vectors which are reported in the publications and which might be used in connection with various embodiments of the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

Definitions

“INTSIG” refers to the amino acid sequences of substantially purified INTSIG obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and human, and from any source, whether natural, synthetic, semi-synthetic, or recombinant

The term “agonist” refers to a molecule which intensifies or mimics the biological activity of INTSIG. Agonists may include proteins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of INTSIG either by directly interacting with INTSIG or by acting on components of the biological pathway in which INTSIG participates.

An “allelic variant” is an alternative form of the gene encoding INTSIG. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. A gene may have none, one, or many allelic variants of its naturally occurring form. Common mutational changes which give rise to allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

“Altered” nucleic acid sequences encoding INTSIG include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as INTSIG or a polypeptide with at least one functional characteristic of INTSIG. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding INTSIG, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide encoding INTSIG. The encoded protein may also be “altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent INTSIG. Deliberate amino acid substitutions may be made on the basis of one or more similarities in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of INTSIG is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, and positively charged amino acids may include lysine and arginine. Amino acids with uncharged polar side chains having similar hydrophilicity values may include: asparagine and glutamine; and serine and threonine. Amino acids with uncharged side chains having similar hydrophilicity values may include: leucine, isoleucine, and valine; glycine and alanine; and phenylalanine and tyrosine.

The terms “amino acid” and “amino acid sequence” can refer to an oligopeptide, a peptide, a polypeptide, or a protein sequence, or a fragment of any of these, and to naturally occurring or synthetic molecules. Where “amino acid sequence” is recited to refer to a sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.

“Amplification” relates to the production of additional copies of a nucleic acid. Amplification may be carried out using polymerase chain reaction (PCR) technologies or other nucleic acid amplification technologies well known in the art.

The term “antagonist” refers to a molecule which inhibits or attenuates the biological activity of INTSIG. Antagonists may include proteins such as antibodies, anticalins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of INTSIG either by directly interacting with INTSIG or by acting on components of the biological pathway in which INTSIG participates.

The term “antibody” refers to intact immunoglobulin molecules as well as to fragments thereof, such as Fab, F(ab′)₂, and Fv fragments, which are capable of binding an epitopic determinant. Antibodies that bind INTSIG polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or oligopeptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

The term “antigenic determinant” refers to that region of a molecule (i.e., an epitope) that makes contact with a particular antibody. When a protein or a fragment of a protein is used to immunize a host animal, numerous regions of the protein may induce the production of antibodies which bind specifically to antigenic determinants (particular regions or three-dimensional structures on the protein). An antigenic determinant may compete with the intact antigen (i.e., the immunogen used to elicit the immune response) for binding to an antibody.

The term “aptamer” refers to a nucleic acid or oligonucleotide molecule that binds to a specific molecular target. Aptamers are derived from an in vitro evolutionary process (e.g., SELEX (Systematic Evolution of Ligands by EXponential Enrichment), described in U.S. Pat. No. 5,270,163), which selects for target-specific aptamer sequences from large combinatorial libraries. Aptamer compositions may be double-stranded or single-stranded, and may include deoxyribonucleotides, ribonucleotides, nucleotide derivatives, or other nucleotide-like molecules. The nucleotide components of an aptamer may have modified sugar groups (e.g., the 2′-OH group of a ribonucleotide maybe replaced by 2′-F or 2′-NH), which may improve a desired property, e.g., resistance to nucleases or longer lifetime in blood. Aptamers may be conjugated to other molecules, e.g., a high molecular weight carrier to slow clearance of the aptamer from the circulatory system. Aptamers may be specifically cross-linked to their cognate ligands, e.g., by photo-activation of a cross-linker (Brody, E. N. and L. Gold (2000) J. Biotechnol. 74:5-13).

The term “intramer” refers to an aptamer which is expressed in vivo. For example, a vaccinia virus-based RNA expression system has been used to express specific RNA aptamers at high levels in the cytoplasm of leukocytes (Blind, M. et al. (1999) Proc. Natl Acad. Sci. USA 96:3606-3610).

The term “spiegelmer” refers to an aptamer which includes L-DNA, L-RNA, or other left-handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides.

The term “antisense” refers to any composition capable of base-pairing with the “sense” (coding) strand of a polynucleotide having a specific nucleic acid sequence. Antisense compositions may include DNA; RNA; peptide nucleic acid (PNA); oligonucleotides having modified backbone. linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2′-methoxyethyl sugars or 2′-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2′-deoxyuracil, or 7-deaza-2′-deoxyguanosine. Antisense molecules may be produced by any method including chemical synthesis or transcription Once introduced into a cell, the complementary antisense molecule base-pairs with a naturally occurring nucleic acid sequence produced by the cell to form duplexes which block either transcription or translation. The designation “negative” or “minus” can refer to the antisense strand, and the designation “positive” or “plus” can refer to the sense strand of a reference DNA molecule.

The term “biologically active” refers to a protein having structural regulatory, or biochemical functions of a naturally occurring molecule. Likewise, “immunologically active” or “immunogenic” refers to the capability of the natural, recombinant, or synthetic INTSIG, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

“Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing. For example, 5′-AGT-3′ pairs with its complement, 3′-TCA-5′.

A “composition comprising a given polynucleotide” and a “composition comprising a given polypeptide” can refer to any composition containing the given polynucleotide or polypeptide. The composition may comprise a dry formulation or an aqueous solution. Compositions comprising polynucleotides encoding INTSIG or fragments of INTSIG may be employed as hybridization probes. The probes maybe stored in freeze-dried form and maybe associated with a stabilizing agent such as a carbohydrate. In hybridizations, the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., sodium dodecyl sulfate; SDS), and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).

“Consensus sequence” refers to a nucleic acid sequence which has been subjected to repeated DNA sequence analysis to resolve uncalled bases, extended using the XL-PCR kit (Applied Biosystems, Foster City Calif.) in the 5′ and/or the 3′ direction, and resequenced, or which has been assembled from one or more overlapping cDNA, EST, or genomic DNA fragments using a computer program for fragment assembly, such as the GELVIEW fragment assembly system (GCG, Madison Wis.) or Phrap (University of Washington, Seattle Wash.). Some sequences have been both extended and assembled to produce the consensus sequence.

“Conservative amino acid substitutions” are those substitutions that are predicted to least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative amino acid substitutions. Original Residue Conservative Substitution Ala Gly, Ser Arg His, Lys Asn Asp, Gln, His Asp Asn, Glu Cys Ala, Ser Gln Asn, Glu, His Glu Asp, Gln, His Gly Ala His Asn, Arg, Gln, Glu Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe, Tyr Tyr His, Phe, Trp Val Ile, Leu, Thr

Conservative amino acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the site of the substitution, and/or (c) the bulk of the side chain.

A “deletion” refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.

The term “derivative” refers to a chemically modified polynucleotide or polypeptide. Chemical modifications of a polynucleotide can include, for example, replacement of hydrogen by an alkyl, acyl, hydroxyl, or amino group. A derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule. A derivative polypeptide is one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.

A “detectable label” refers to a reporter molecule or enzyme that is capable of generating a measurable signal and is covalently or noncovalently joined to a polynucleotide or polypeptide.

“Differential expression” refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons may be carried out between, for example, a treated and an untreated sample, or a diseased and a normal sample.

“Exon shuffling” refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortment of stable substructures, thus allowing acceleration of the evolution of new protein functions.

A “fragment” is a unique portion of INTSIG or a polynucleotide encoding INTSIG which can be identical in sequence to, but shorter in length than, the parent sequence. A fragment may comprise p to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from about 5 to about 1000 contiguous nucleotides or amino acid residues. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, ay be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous nucleotides or amino acid residues in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing, tables, and figures, may be encompassed by the present embodiments.

A fragment of SEQ ID NO:46-90 can comprise a region of unique polynucleotide sequence that specifically identifies SEQ ID NO:46-90, for example, as distinct from any other sequence in the genome from which the fragment was obtained. A fragment of SEQ ID NO:46-90 can be employed in one or more embodiments of methods of the invention, for example, in hybridization and amplification technologies and in analogous methods that distinguish SEQ ID NO:46-90 from related polynucleotides. The precise length of a fragment of SEQ ID NO:46-90 and the region of SEQ ID NO:46-90 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

A fragment of SEQ ID NO:1-45 is encoded by a fragment of SEQ ID NO:46-90. A fragment of SEQ ID NO:1-45 can comprise a region of unique amino acid sequence that specifically identifies SEQ ID NO:1-45. For example, a fragment of SEQ ID NO:1-45 can be used as an immunogenic peptide for the development of antibodies that specifically recognize SEQ ID NO:1-45. The precise length of a fragment of SEQ ID NO:1-45 and the region of SEQ ID NO:1-45 to which the fragment corresponds can be determined based on the intended purpose for the fragment using one or more analytical methods described herein or otherwise known in the art.

A “full length” polynucleotide is one containing at least a translation initiation codon (e.g., methionine) followed by an open reading frame and a translation termination codon. A “full length” polynucleotide sequence encodes a “full length” polypeptide sequence.

“Homology” refers to sequence similarity or, interchangeably, sequence identity, between two or more polynucleotide sequences or two or more polypeptide sequences.

The terms “percent identity” and “% identity,” as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.

Percent identity between polynucleotide sequences may be determined using one or more computer algorithms or programs known in the art or described herein For example, percent identity can be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison Wis.). CLUSTAL V is described in Higgins, D. G. and P. M. Sharp (1989; CABIOS 5:151-153) and in Higgins, D. G. et al. (1992; CABIOS 8:189-191). For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and “diagonals saved”=4. The “weighted” residue weight table is selected as the default Percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polynucleotide sequences.

Alternatively, a suite of commonly used and freely available sequence comparison algorithms which can be used is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, Md., and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including “blastn,” that is used to align a known polynucleotide sequence with other polynucleotide sequences from a variety of databases. Also available is a tool called “BLAST 2 Sequences” that is used for direct pairwise comparison of two nucleotide sequences. “BLAST 2 Sequences” can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/12.html. The “BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the “BLAST 2 Sequences” tool Version 2.0.12 (Apr. 21, 2000) set at default parameters. Such default parameters maybe, for example:

-   -   Matrix: BLOSUM62     -   Reward for match: 1     -   Penalty for mismatch: −2     -   Open Gap: 5 and Extension Gap: 2 penalties     -   Gap x drop-off: 50     -   Expect: 10     -   Word Size: 11     -   Filter: on

Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures, or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.

The phrases “percent identity” and “% identity,” as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the charge and hydrophobicity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide.

Percent identity between polypeptide sequences maybe determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=1, gap penalty=3, window=5, and “diagonals saved”=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polypeptide sequence pairs.

Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the “BLAST 2 Sequences” tool Version 2.0.12 (Apr. 21, 2000) with blastp set at default parameters. Such default parameters may be, for example:

-   -   Matrix: BLOSUM62     -   Open Gap: 11 and Extension Gap: 1 penalties     -   Gap x drop-off 50     -   Expect: 10     -   Word Size: 3     -   Filter: on

Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40,at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured. “Human artificial chromosomes” (HACs) are linear microchromosomes which may contain DNA sequences of about 6 kb to 10 Mb in size and which contain all of the elements required for chromosome replication, segregation and maintenance.

The term “humanized antibody” refers to an antibody molecule in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.

“Hybridization” refers to the process by which a polynucleotide strand anneals with a complementary strand through base pairing under defined hybridization conditions. Specific hybridization is an indication that two nucleic acid sequences share a high degree of complementarity. Specific hybridization complexes form under permissive annealing conditions and remain hybridized after the “washing” step(s). The washing step(s) is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid strands that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency, and therefore hybridization specificity. Permissive annealing conditions occur, for example, at 68° C, in the presence of about 6×SSC, about 1% (wtv) SDS, and about 100 μg/ml sheared, denatured salmon sperm DNA.

Generally, stringency of hybridization is expressed, in part, with reference to the temperature under which the wash step is carried out. Such wash temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating T_(m) and conditions for nucleic acid hybridization are well known and can be found in Sambrook, J. et al. (1989) Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; specifically see volume 2, chapter 9.

High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68° C. in the presence of about 0.2×SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65° C., 60° C., 55° C., or 42° C. may be used. SSC concentration may be varied from about 0.1 to 2×SSC, with SDS being present at about 0.1%. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, sheared and denatured salmon sperm DNA at about 100-200 μg/ml. Organic solvent, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as for RNA:DNA hybridizations. Useful variations on these wash conditions will be readily apparent to those of ordinary skill in the art Hybridization, particularly under high stringency conditions, maybe suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their encoded polypeptides.

The term “hybridization complex” refers to a complex formed between two nucleic acids by virtue of the formation of hydrogen bonds between complementary bases. A hybridization complex may be formed in solution (e.g., C₀t or R₀t analysis) or formed between one nucleic acid present in solution and another nucleic acid immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).

The words “insertion” and “addition” refer to changes in an amino acid or polynucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively.

“Immune response” can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytolines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.

An “immunogenic fragment” is a polypeptide or oligopeptide fragment of INTSIG which is capable of eliciting an immune response when introduced into a living organism, for example, a mammal. The term “immunogenic fragment” also includes any polypeptide or oligopeptide fragment of INTSIG which is useful in any of the antibody production methods disclosed herein or known in the art.

The term “microarray” refers to an arrangement of a plurality of polynucleotides, polypeptides, antibodies, or other chemical compounds on a substrate.

The terms “element” and “array element” refer to a polynucleotide, polypeptide, antibody, or other chemical compound having a unique and defined position on a microarray.

The term “modulate” refers to a change in the activity of INTSIG. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of INTSIG.

The phrases “nucleic acid” and “nucleic acid sequence” refer to a nucleotide, oligonucleotide, polynucleotide, or any fragment thereof. These phrases also refer to DNA or RNA of genomic or synthetic origin which maybe single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material.

“Operably linked” refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with a second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.

“Peptide nucleic acid” (PNA) refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about S nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell.

“Post-translational modification” of an INTSIG may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu of INTSIG.

“Probe” refers to nucleic acids encoding INTSIG, their complements, or fragments thereof, which are used to detect identical, allelic or related nucleic acids. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. “Primers” are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid, e.g., by the polymerase chain reaction (PCR).

Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the tables, figures, and Sequence Listing, maybe used.

Methods for preparing and using probes and primers are described in the references, for example Sambrook, J. et al. (1989; Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.), Ausubel, F. M. et al. (1999; Short Protocols in Molecular Biology, 4^(th) ed., John Wiley & Sons, New York N.Y.), and Innis, M. et al. (1990; PCR Protocols, A Guide to Methods and Applications, Academic Press, San Diego Calif.). PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge Mass.).

Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas Tex.) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge Mass.) allows the user to input a “mispriming library,” in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identity fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.

A “recombinant nucleic acid” is a nucleic acid that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.

Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

A “regulatory element” refers to a nucleic acid sequence usually derived from untranslated regions of a gene and includes enhancers, promoters, introns, and 5′ and 3′ untranslated regions (UTRs). Regulatory elements interact with host or viral proteins which control transcription, translation, or RNA stability.

“Reporter molecules” are chemical or biochemical moieties used for labeling a nucleic acid, amino acid, or antibody. Reporter molecules include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

An “RNA equivalent,” in reference to a DNA molecule, is composed of the same linear sequence of nucleotides as the reference DNA molecule with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

The term “sample” is used in its broadest sense. A sample suspected of containing INTSIG, nucleic acids encoding INTSIG, or fragments thereof may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print; etc.

The terms “specific binding” and “specifically binding” refer to that interaction between a protein or peptide and an agonist, an antibody, an antagonist, a small molecule, or any natural or synthetic binding composition. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope “A,” the presence of a polypeptide comprising the epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.

The term “substantially purified” refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least about 60% free, preferably at least about 75% free, and most preferably at least about 90% free from other components with which they are naturally associated.

A “substitution” refers to the replacement of one or more amino acid residues or nucleotides by different amino acid residues or nucleotides, respectively.

“Substrate” refers to any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.

A “transcript image” or “expression profile” refers to the collective pattern of gene expression by a particular cell type or tissue under given conditions at a given time.

“Transformation” describes a process by which exogenous DNA is introduced into a recipient cell. Transformation may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, bacteriophage or viral infection, electroporation, heat shock, lipofection, and particle bombardment. The term “transformed cells” includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.

A “transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. In another embodiment, the nucleic acid can be introduced by infection with a recombinant viral vector, such as a lentiviral vector (Lois, C. et al. (2002) Science 295:868-872). The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.

A “variant” of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 40% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length A variant may be described as, for example, an “allelic” (as defined above), “splice,” “species,” or “polymorphic” variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotides that vary from one species to another. The resulting polypeptides will generally have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymorphic variants also may encompass “single nucleotide polymorphisms” (SNPs) in which the polynucleotide sequence varies by one nucleotide base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

A “variant” of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length of one of the polypeptides.

The Invention

Various embodiments of the invention include new human intracellular signaling molecules (INTSIG), the polynucleotides encoding INTSIG, and the use of these compositions for the diagnosis, treatment, or prevention of cell proliferative, endocrine, autoimmune/inflammatory, neurological, gastrointestinal, reproductive, developmental, and vesicle trafficking disorders.

Table 1 summarizes the nomenclature for the full length polynucleotide and polypeptide embodiments of the invention. Each polynucleotide and its corresponding polypeptide are correlated to a single Incyte project identification number (Incyte Project ID). Each polypeptide sequence is denoted by both a polypeptide sequence identification number (Polypeptide SEQ ID NO:) and an Incyte polypeptide sequence number (Incyte Polypeptide ID) as shown. Each polynucleotide sequence is denoted by both a polynucleotide sequence identification number (Polynucleotide SEQ ID NO:) and an Incyte polynucleotide consensus sequence number (Incyte Polynucleotide ID) as shown. Column 6 shows the Incyte ID numbers of physical, full length clones corresponding to the polypeptide and polynucleotide sequences of the invention. The full length clones encode polypeptides which have at least 95% sequence identity to the polypeptide sequences shown in column 3.

Table 2 shows sequences with homology to the polypeptides of the invention as identified by BLAST analysis against the GenBank protein (genpept) database and the PROTEOME database. Columns 1 and 2 show the polypeptide sequence identification number (Polypeptide SEQ ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for polypeptides of the invention. Column 3 shows the GenBank identification number (GenBank ID NO:) of the nearest GenBank homolog and the PROTEOME database identification numbers (PROTEOME ID NO:) of the nearest PROTEOME database homologs. Column 4 shows the probability scores for the matches between each polypeptide and its homolog(s). Column 5 shows the annotation of the GenBank and PROTEOME database homolog(s) along with relevant citations where applicable, all of which are expressly incorporated by reference herein.

Table 3 shows various structural features of the polypeptides of the invention. Columns 1 and 2 show the polypeptide sequence identification number (SEQ ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for each polypeptide of the invention. Column 3 shows the number of amino acid residues in each polypeptide. Column 4 shows potential phosphorylation sites, and column 5 shows potential glycosylation sites, as determined by the MOTIFS program of the GCG sequence analysis software package (Genetics Computer Group, Madison Wis.). Column 6 shows amino acid residues comprising signature sequences, domains, and motifs. Column 7 shows analytical methods for protein structure/function analysis and in some cases, searchable databases to which the analytical methods were applied.

Together, Tables 2 and 3 summarize the properties of polypeptides of the invention, and these properties establish that the claimed polypeptides are GTPase-associated proteins. For example, SEQ ID NO:1 is 53% identical, from residue R190 to residue B706, to human guanine nucleotide regulatory protein (GenBank ID g484102) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 1.3e-129, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:1 also contains a PH domain, a RhoGEF domain, and an SH3 domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from additional BLAST analyses provide further corroborative evidence that SEQ ID NO:1 is a guanine nucleotide regulatory protein.

As another example, SEQ ID NO:6 is 58% identical, from residue L225 to residue C1845, to human nuclear dual-specificity phosphatase (GenBank ID g3015538) as determined by BLAST. The BLAST probability score is 0.0. SEQ ID NO:2 also contains DENN (AEX-3) and PH domains as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. Data from further BLAST analyses provide corroborative evidence that SEQ ID NO:6 is a dual-specificity phosphatase.

As another example, SEQ ID NO:10 is 99% identical, from residue A44 to residue M316, to human TRAF4 associated factor 1 (GenBank ID g458001 1) as determined by BLAST. The BLAST probability score is 1.0e-138. In addition, SEQ ID NO:10 is 50% identical, from residue M18 to residue V775, to murine semaphorin cytoplasmic domain-associated protein 3B (GenBank ID g6651021) as determined by BLAST. The BLAST probability score is 9.6e-51. SEQ ID NO:10 also contains a PDZ domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. Data from BLAST-PRODOM, BLIMPS, and MOTIFS analyses provide filer corroborative evidence that SEQ ID NO:10 is a signal transduction molecule.

As another example, SEQ ID NO:15 is 79% identical, from residue M1 to residue L917, to mouse PDZ-RGS3 protein, (GenBank ID g13774477) as determined by BLAST. The BLAST probability score is 0.0. The PDZ-RGS3 protein, binds B ephrins through a PDZ domain, and has a regulator of heterotrimeric G protein signaling (RGS) domain (Lu, Q. et al. (2001) Cell 105 (1), 69-79). SEQ ID NO:15 also contains a regulator of G protein signaling domain and a PDZ domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. Data from BLIMPS, MOTIFS, and further BLAST analyses provide corroborative evidence that SEQ ID NO:15 is a PDZ-RGS3 protein.

As another example, SEQ ID NO:24 is 91% identical, from residue MI to residue D1023, to p116Rip (GenBank ID g1657837), a Rho-interacting GDP/GTP exchange factor, as determined by BLAST. The BLAST probability score is 0.0. SEQ ID NO:24 also contains a PH domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. Data from additional BLAST analysis provide firer corroborative evidence that SEQ ID NO:24 is a Rho-binding protein.

As another example, SEQ ID NO:27 is 82% identical, from residue P56 to residue L1123, to the sorbin and SH3 domain-containing gene (GenBank ID g13650131) as determined by BLAST. The BLAST probability score is 0.0, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:27 contains an SH3 and a sorbin domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. Data from BUMPS and BLAST analyses provide further corroborative evidence that SEQ ID NO:27 is an SH3 domain-containing protein.

As another example, SEQ ID NO:30, SEQ ID NO:32-36, and SEQ ID NO:39 have significant homology to Rattus norvepicus synaptic ras GTPase-activating protein SynGAP (GenBank ID g2935448), as determined by BLAST. SEQ ID NO:30 is 95% identical to GenBank ID g2935448 from residue M1 to residue P1143. SEQ ID NO:32 is 97% identical to GenBank ID g2935448 from residue M1 to residue V1308. SEQ ID NO:33 is 99% identical to GenBank ID g2935448 from residue M1 to residue V1279. SEQ ID NO:34 is 99% identical to GenBank ID g2935448 from residue M1 to residue V1293. SEQ ID NO:35 is 99% identical to GenBank ID g2935448 from residue M1 to residue L387 and 98% identical from residue V416 to residue P1157. SEQ ID NO:36 is 98% identical to GenBank ID g2935448 from residue M1 to residue P1128. SEQ ID NO:39 is 99% identical to GenBank ID g2935448 from residue M1 to residue L545 and 98% identical from residue V574 to residue V1322. (See Table 2.) The BLAST probability score for each of SEQ ID NO:30, SEQ ID NO:32-36, and SEQ ID NO:39 is 0.0, which indicates the probability of obtaining the observed polypeptide sequence alignments by chance. SEQ ID NO:30, SEQ ID NO:32-36, and SEQ ID NO:39 are identified as GTPase activating proteins, as determined by BLAST analysis using the PROTEOME database. SEQ ID NO:30, SEQ ID NO:32-36, and SEQ ID NO:39 each contain a Ras GTPase-activating proteins signature and profile domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database. (See Table 3.) Data from BLIMPS, MOTIFS, and PROFHESCAN analyses provide further corroborative evidence that SEQ ID NO:30, SEQ ID NO:32-36, and SEQ ID NO:39 are GTPase activating proteins.

As another example, SEQ ID NO:42 is 97% identical, from residue M33 to residue S309, to human Ras like GTPase (GenBank ID g2117166) as determined by BLAST. The BLAST probability score is 4.5e-145. SEQ ID NO:42 is a GTP-binding protein, as determined by BLAST analysis using the PROTEOME database. SEQ ID NO:42 also contains a Ras family domain as determined by 10 searching for statistically significant matches in the hidden Markov model (MM)-based PFAM database. Data from BLIMPS, MOTIFS and additional BLAST analyses provide further corroborative evidence that SEQ ID NO:42 is a Ras family GTPase. SEQ ID NO:2-5, SEQ ID NO:7-9, SEQ ID NO:11-14, SEQ ID NO:16-23, SEQ ID NO:25-26, SEQ ID NO:28-29, SEQ ID NO:31, SEQ ID NO:37-38, and SEQ ID NO:40-41 were analyzed and annotated in a similar manner. The algorithms and parameters for the analysis of SEQ ID NO: 1-45 are described in Table 7.

As shown in Table 4, the full length polynucleotide embodiments were assembled using cDNA sequences or coding (exon) sequences derived from genomic DNA, or any combination of these two types of sequences. Column 1 lists the polynucleotide sequence identification number (Polynucleotide SEQ ID NO:), the corresponding Incyte polynucleotide consensus sequence number (Incyte ID) for each polynucleotide of the invention, and the length of each polynucleotide sequence in basepairs. Column 2 shows the nucleotide start (5′) and stop (3′) positions of the cDNA and/or genomic sequences used to assemble the full length polynucleotide embodiments, and of fragments of the polynucleotides which are useful, for example, in hybridization or amplification technologies that identify SEQ ID NO:46-90 or that distinguish between SEQ ID NO:46-90 and related polynucleotides.

The polynucleotide fragments described in Column 2 of Table 4 may refer specifically, for example, to Incyte cDNAs derived from tissue-specific cDNA libraries or from pooled cDNA libraries. Alternatively, the polynucleotide fragments described in column 2 may refer to GenBank cDNAs or ESTs which contributed to the assembly of the fall length polynucleotides. In addition, the polynucleotide fragments described in column 2 may identify sequences derived from the ENSEMBL (The Sanger Centre, Cambridge, UK) database (i.e., those sequences including the designation “ENST”). Alternatively, the polynucleotide fragments described in column 2 may be derived from the NCBI RefSeq Nucleotide Sequence Records Database (i.e., those sequences including the designation “NM” or “NT”) or the NCBI RefSeq Protein Sequence Records (i.e., those sequences including the designation “NP”). Alternatively, the polynucleotide fragments described in column 2 may refer to assemblages of both cDNA and Genscan-predicted exons brought together by an “exon stitching” algorithm. For example, a polynucleotide sequence identified as FL_XXXXXX_N_(1—)N_(2—)YYYYY_(—N) _(3—)N₄ represents a “stitched” sequence in which XXXXXX is the identification number of the cluster of sequences to which the algorithm was applied, and YYYYY is the number of the prediction generated by the algorithm, and N_(1,2,3 . . .) , if present, represent specific exons that may have been manually edited during analysis (See Example V). Alternatively, the polynucleotide fragments in column 2 may refer to assemblages of exons brought together by an “exon-stretching” algorithm. For example, a polynucleotide sequence identified as FLXXXXXX_gAAAAA_gBBBBB_(—)1_N is, a “stretched” sequence, with being the Incyte project identification number, gAAAAA being the GenBank identification number of the human genomic sequence to which the “exon-stretching” algorithm was applied, gBBBBB being the GenBank identification number or NCBI RefSeq identification number of the nearest GenBank protein homolog, and N referring to specific exons (See Example V). In instances where a RefSeq sequence was used as a protein homolog for the “exon-stretching” algorithm, a RefSeq identifier (denoted by “NM,” “NP,” or “NT”) may be used in place of the GenBank identifier (i.e., gBBBBB).

Alternatively, a prefix identifies component sequences that were hand-edited, predicted from genomic DNA sequences, or derived from a combination of sequence analysis methods. The following Table lists examples of component sequence prefixes and corresponding sequence analysis methods associated with the prefixes (see Example IV and Example V). Prefix Type of analysis and/or examples of programs GNN, GFG, Exon prediction from genomic sequences using, ENST for example, GENSCAN (Stanford University, CA, USA) or FGENES (Computer Genomics Group, The Sanger Centre, Cambridge, UK) GBI Hand-edited analysis of genomic sequences. FL Stitched or stretched genomic sequences (see Example V). INCY Full length transcript and exon prediction from mapping of EST sequences to the genome. Genomic location and EST composition data are combined to predict the exons and resulting transcript

In some cases, Incyte cDNA coverage redundant with the sequence coverage shown in Table 4 was obtained to confirm the final consensus polynucleotide sequence, but the relevant Incyte cDNA identification numbers are not shown.

Table 5 shows the representative cDNA libraries for those full length polynucleotides which were assembled using Incyte cDNA sequences. The representative cDNA library is the Incyte cDNA library which is most frequently represented by the Incyte cDNA sequences which were used to assemble and confirm the above polynucleotides. The tissues and vectors which were used to construct the cDNA libraries shown in Table 5 are described in Table 6.

Table 8 shows single nucleotide polymorphisms (SNPs) found in polynucleotide sequences of the invention, along with allele frequencies in different human populations. Columns 1 and 2 show the polynucleotide sequence identification number (SEQ ID NO:) and the corresponding Incyte project identification number (PID) for polynucleotides of the invention. Column 3 shows the Incyte identification number for the EST in which the SNP was detected (EST ID), and column 4 shows the identification number for the SNP (SNP ID). Column 5 shows the position within the EST sequence at which the SNP is located (EST SNP), and column 6 shows the position of the SNP within the full-length polynucleotide sequence (CB1 SNP). Column 7 shows the allele found in the EST sequence. Columns 8 and 9 show the two alleles found at the SNP site. Column 10 shows the amino acid encoded by the codon including the SNP site, based upon the allele found in the EST. Columns 11-14 show the frequency of allele 1 in four different human populations. An entry of n/d (not detected) indicates that the frequency of allele 1 in the population was too low to be detected, while n/a (not available) indicates that the allele frequency was not determined for the population.

The invention also encompasses INTSIG variants. A preferred INTSIG variant is one which has at least about 80%, or alternatively at least about 90%, or even at least about 95% amino acid sequence identity to the INTSIG amino acid sequence, and which contains at least one functional or structural characteristic of INTSIG.

Various embodiments also encompass polynucleotides which encode INTSIG. In a particular embodiment, the invention encompasses a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:46-90, which encodes INTSIG. The polynucleotide sequences of SEQ ID NO:46-90, as presented in the Sequence Listing, embrace the equivalent RNA sequences, wherein occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

The invention also encompasses variants of a polynucleotide encoding INTSIG. In particular, such a variant polynucleotide will have at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to a polynucleotide encoding INTSIG. A particular aspect of the invention encompasses a variant of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO:46-90 which has at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to a nucleic acid sequence selected from the group consisting of SEQ IID NO:46-90. Any one of the polynucleotide variants described above can encode a polypeptide which contains at least one functional or structural characteristic of INTSIG.

In addition, or in the alternative, a polynucleotide variant of the invention is a splice variant of a polynucleotide encoding INTSIG. A splice variant may have portions which have significant sequence identity to a polynucleotide encoding INTSIG, but will generally have a greater or lesser number of polynucleotides due to additions or deletions of blocks of sequence arising from alternate splicing of exons during mRNA processing. A splice variant may have less than about 70%, or alternatively less than about 60%, or alternatively less than about 50% polynucleotide sequence identity to a polynucleotide encoding INTSIG over its entire length; however, portions of the splice variant will have at least about 70%, or alternatively at least about 85%, or alternatively at least about 95%, or alternatively 100% polynucleotide sequence identity to portions of the polynucleotide encoding INTSIG. For example, a polynucleotide comprising a sequence of SEQ ID NO:54 and a polynucleotide comprising a sequence of SEQ ID NO:90 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO:57 and a polynucleotide comprising a sequence of SEQ ID NO:59 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO:69 and a polynucleotide comprising a sequence of SEQ ID NO:70 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO:75, a polynucleotide comprising a sequence of SEQ ID NO:77, a polynucleotide comprising a sequence of SEQ ID NO:78, a polynucleotide comprising a sequence of SEQ ID NO:79, a polynucleotide comprising a sequence of SEQ ID NO:80, a polynucleotide comprising a sequence of SEQ ID NO:81, and a polynucleotide comprising a sequence of SEQ ID NO:84 are splice variants of each other; and a polynucleotide comprising a sequence of SEQ ID NO:76 and a polynucleotide comprising a sequence of SEQ ID NO:88 are splice variants of each other. Any one of the splice variants described above can encode a polypeptide which contains at least one functional or structural characteristic of INTSIG.

It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of polynucleotide sequences encoding INTSIG, some bearing minimal similarity to the polynucleotide sequences of any known and naturally occurring gene, may be produced. Thus, the invention contemplates each and every possible variation of polynucleotide sequence that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code as applied to the polynucleotide sequence of naturally occurring INTSIG, and all such variations are to be considered as being specifically disclosed.

Although polynucleotides which encode INTSIG and its variants are generally capable of hybridizing to polynucleotides encoding naturally occurring INTSIG under appropriately selected conditions of stringency, it may be advantageous to produce polynucleotides encoding INTSIG or its derivatives possessing a substantially different codon usage, e.g., inclusion of non-naturally occurring codons. Codons maybe selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host. Other reasons for substantially altering the nucleotide sequence encoding INTSIG and its derivatives without altering the encoded amino acid sequences include the production of RNA transcripts having more desirable properties, such as a greater half-life, than transcripts produced from the naturally occurring sequence.

The invention also encompasses production of polynucleotides which encode INTSIG and INTSIG derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic polynucleotide may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a polynucleotide encoding INTSIG or any fragment thereof.

Embodiments of the invention can also include polynucleotides that are capable of hybridizing to the claimed polynucleotides, and, in particular, to those having the sequences shown in SEQ ID NO:46-90 and fragments thereof, under various conditions of stringency (Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) Methods Enzymol. 152:507-511). Hybridization conditions, including annealing and wash conditions, are described in “Definitions.”

Methods for DNA sequencing are well known in the art and may be used to practice any of the embodiments of the invention The methods may employ such enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (US Biochemical, Cleveland Ohio), Taq polymerase (Applied Biosystems), thermostable T7 polymerase (Amersham Biosciences, Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Invitrogen, Carlsbad Calif.). Preferably, sequence preparation is automated with machines such as the MICROLAB 2200 liquid transfer system (Hamilton, Reno Nev.), PTC200 thermal cycler (MJ Research, Watertown Mass.) and ABI CATALYST 800 thermal cycler (Applied Biosystems). Sequencing is then carried out using either the ABI 373 or 377 DNA sequencing system (Applied Biosystems), the MEGABACE 1000 DNA sequencing system (Amersham Biosciences), or other systems known in the art. The resulting sequences are analyzed using a variety of algorithms which are well known in the art (Ausubel et al., supra, ch. 7; Meyers, R. A. (1995) Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp. 856-853).

The nucleic acids encoding INTSIG may be extended utilizing a partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements. For example, one method which may be employed, restriction-site PCR, uses universal and nested primers to amplify unknown sequence from genomic DNA within a cloning vector (Sarkar, G. (1993) PCR Methods Applic. 2:318-322). Another method, inverse PCR, uses primers that extend in divergent directions to amplify unknown sequence from a circularized template. The template is derived from restriction fragments comprising a known genomic locus and surrounding sequences (Triglia, T. et al. (1988) Nucleic Acids Res. 16:8186). A third method, capture PCR, involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA (Lagerstrom, M. et al. (1991) PCR Methods Applic. 1:111-119). In this method, multiple restriction enzyme digestions and ligations may be used to insert an engineered double-stranded sequence into a region of unknown sequence before performing PCR. Other methods which may be used to retrieve unknown sequences are known in the art (Parker, J. D. et al. (1991) Nucleic Acids Res. 19:3055-3060). Additionally, one may use PCR, nested primers, and PROMOTEFINDER libraries (Clontech, Palo Alto Calif.) to walk genomic DNA. This procedure avoids the need to screen libraries and is useful in finding intron/exon junctions. For all PCR-based methods, primers maybe designed using commercially available software, such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth M) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68° C. to 72° C.

When screening for full length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. In addition, random-primed libraries, which often include sequences containing the 5′ regions of genes, are preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into 5′ non-transcribed regulatory regions.

Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products. In particular, capillary sequencing may employ flowable polymers for electrophoretic separation, four different nucleotide-specific, laser-stimulated fluorescent dyes, and a charge coupled device camera for detection of the emitted wavelengths. Output/light intensity may be converted to electrical signal using appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR, Applied Biosystems), and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled. Capillary electrophoresis is especially preferable for sequencing small DNA fragments which may be present in limited amounts in a particular sample.

In another embodiment of the invention, polynucleotides or fragments thereof which encode INTSIG may be cloned in recombinant DNA molecules that direct expression of INTSIG, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other polynucleotides which encode substantially the same or a functionally equivalent polypeptides may be produced and used to express INTSIG.

The polynucleotides of the invention can be engineered using methods generally known in the art in order to alter INTSIG-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.

The nucleotides of the present invention may be subjected to DNA shuffling techniques such as MOLECULARBREEDING (Maxygen Inc., Santa Clara Calif.; described in U.S. Pat. No. 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F. C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of INTSIG, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and farther subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through “artificial” breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.

In another embodiment, polynucleotides encoding INTSIG may be synthesized, in whole or in part, using one or more chemical methods well known in the art (Caruthers, M. H. et al. (1980) Nucleic Acids Symp. Ser. 7:215-223; Horn, T. et al. (1980) Nucleic Acids Symp. Ser. 7:225-232). Alternatively, INTSIG itself or a fragment thereof may be synthesized using chemical methods known in the art. For example, peptide synthesis can be performed using various solution-phase or solid-phase techniques (Creighton, T. (1984) Proteins, Structures and Molecular Properties, WH Freeman, New York N.Y., pp. 55-60; Roberge, J. Y. et al. (1995) Science 269:202-204). Automated synthesis maybe achieved using the ABI 431A peptide synthesizer (Applied Biosystems). Additionally, the amino acid sequence of INTSIG, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide or a polypeptide having a sequence of a naturally occurring polypeptide.

The peptide may be substantially purified by preparative high performance liquid chromatography (Chiez, R. M. and F. Z. Regnier (1990) Methods Enzymol. 182:392-421). The composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing (Creighton, supra, pp. 28-53).

In order to express a biologically active INTSIG, the polynucleotides encoding INTSIG or derivatives thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. These elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5′ and 3′untranslated regions in the vector and in polynucleotides encoding INTSIG. Such elements may vary in their strength and specificity. Specific initiation signals may also be used to achieve more efficient translation of polynucleotides encoding INTSIG. Such signals include the ATG initiation codon and adjacent sequences, e.g. the Kozak sequence. In cases where a polynucleotide sequence encoding INTSIG and its initiation codon and upstream regulatory sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals including an in-frame ATG initiation codon should be provided by the vector. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular host cell system used (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162).

Methods which are well known to those skilled in the art may be used to construct expression vectors containing polynucleotides encoding INTSIG and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination (Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y., ch. 4, 8, and 16-17; Ausubel et al., sura, ch. 1, 3, and 15).

A variety of expression vector/host systems maybe utilized to contain and express polynucleotides encoding INTSIG. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems (Sambrook, supra; Ausubel et al., supra; Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355). Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of polynucleotides to the targeted organ, tissue, or cell population (Di Nicola, M. et al (1998) Cancer Gen. Ther. 5:350-356; Yu, M. et al. (1993) Proc. Natl Acad. Sci. USA 90:6340-6344; Buller, R. M. et al. (1985) Nature 317:813-815; McGregor, D. P. et al (1994) Mol. Immunol 31:219-226; Verma, I. M. and N. Somia (1997) Nature 389:239-242). The invention is not limited by the host cell employed.

In bacterial systems, a number of cloning and expression vectors may be selected depending upon the use intended for polynucleotides encoding INTSIG. For example, routine cloning, subcloning, and propagation of polynucleotides encoding INTSIG can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla Calif.) or PSPORT1 plasmid (Invitrogen). Ligation of polynucleotides encoding INTSIG into the vector's multiple cloning site disrupts the lacZ gene, allowing a colorimetric screening procedure for identification of transformed bacteria containing recombinant molecules. In addition, these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence (Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem 264:5503-5509). When large quantities of INTSIG are needed, e.g. for the production of antibodies, vectors which direct high level 5 expression of INTSIG may be used. For example, vectors containing the strong, inducible SP6 or T7 bacteriophage promoter may be used.

Yeast expression systems maybe used for production of INTSIG. A number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris. In addition, such 10 vectors direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign polynucleotide sequences into the host genome for stable propagation (Ausubel et al., supra; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; Scorer, C. A. et al. (1994) Bio/Technology 12:181-184).

Plant systems may also be used for expression of INTSIG. Transcription of polynucleotides encoding INTSIG may be driven by viral promoters, e.g., the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters maybe used (Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection (The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196).

In mammalian cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, polynucleotides encoding INTSIG may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain infective virus which expresses INTSIG in host cells (Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells. SV40 or EBV-based vectors may also be used for high-level protein expression.

Human artificial chromosomes (HACs) may also be employed to deliver larger fragments of DNA than can be contained in and expressed from a plasmid. HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes (Harrington, J. J. et al. (1997) Nat Genet. 15:345-355).

For long term production of recombinant proteins in mammalian systems, stable expression of INTSIG in cell lines is preferred. For example, polynucleotides encoding INTSIG can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells maybe allowed to grow for about 1 to 2 days in enriched media before being switched to selective media. The purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.

Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk⁻ and apr⁻ cells, respectively (Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823). Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate; neo confers resistance to the aminoglycosides neomycin and G-418; and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14). Additional selectable genes have been described, e.g., trpB and hisD, which alter cellular requirements for metabolites (Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051). Visible markers, e.g., anthocyanins, green fluorescent proteins (GFP; Clontech), β-glucuronidase and its substrate β-glucuronide, or luciferase and its substrate luciferin may be used. These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131).

Although the presence/absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding INTSIG is inserted within a marker gene sequence, transformed cells containing polynucleotides encoding INTSIG can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding INTSIG under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

In general, host cells that contain the polynucleotide encoding INTSIG and that express INTSIG may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.

Immunological methods for detecting and measuring the expression of INTSIG using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassay (RIAs), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on INTSIG is preferred, but a competitive binding assay may be employed. These and other assays are well known in the art (Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual, APS Press, St. Paul Minn., Sect. IV; Coligan, J. E. et al (1997) Current Protocols in Immunology, Greene Pub. Associates and Wiley-Interscience, New York N.Y.; Pound, J. D. (1998) Immunochemical Protocols, Humana Press, Totowa N.J.).

A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding INTSIG include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide. Alternatively, polynucleotides encoding INTSIG, or any fragments thereof, may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures maybe conducted using a variety of commercially available kits, such as those provided by Amersham Biosciences, Promega (Madison Wis.), and US Biochemical. Suitable reporter molecules or labels which may be used for ease of detection include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

Host cells transformed with polynucleotides encoding INTSIG may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence nd/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode INTSIG may be designed to contain signal sequences which direct secretion of INTSIG through a prokaryotic or eukaryotic cell membrane.

In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted polynucleotides or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” or “pro” form of the protein may also be used to specify protein targeting, folding, and/or activity. Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and W138) are available from the American Type Culture Collection (ATCC, Manassas Va.) and maybe chosen to ensure the correct modification and processing of the foreign protein.

In another embodiment of the invention, natural, modified, or recombinant polynucleotides encoding INTSIG may be ligated to a heterologous sequence resulting in translation of a fusion protein in any of the aforementioned host systems. For example, a chimeric INTSIG protein containing a heterologous moiety that can be recognized by a commercially available antibody may facilitate the screening of peptide libraries for inhibitors of INTSIG activity. Heterologous protein and peptide moieties may also facilitate purification of fusion proteins using commercially available affinity matrices. Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP), 6-His, FLAG, c-myc, and hemagglutinin (HA). GST, MBP, Trx, CBP, and 6-His enable purification of their cognate fusion proteins on immobilized glutathione, maltose, phenylarsine oxide, calmodulin, and metal-chelate resins, respectively. FLAG, c-myc, and hemagglutinin (HA) enable immunoaffinity purification of fusion proteins using commercially available monoclonal and polyclonal antibodies that specifically recognize these epitope tags. A fusion protein may also be engineered to contain a proteolytic cleavage site located between the INTSIG encoding sequence and the heterologous protein sequence, so that INTSIG may be cleaved away from the heterologous moiety following purification. Methods for fusion protein expression and purification are discussed in Ausubel et al (supra, ch 10 and 16). A variety of commercially available kits may also be used to facilitate expression and purification of fusion proteins.

In another embodiment, synthesis of radiolabeled INTSIG may be achieved in vitro using the TNT rabbit reticulocyte lysate or wheat germ extract system (Promega). These systems couple transcription and translation of protein-coding sequences operably associated with the 17, 13, or SP6 promoters. Translation takes place in the presence of a radiolabeled amino acid precursor, for example, ³⁵S-methionine.

INTSIG, fragments of INTSIG, or variants of INTSIG maybe used to screen for compounds that specifically bind to INTSIG. One or more test compounds may be screened for specific binding to INTSIG. In various embodiments, 1, 2, 3, 4, 5, 10, 20, 50, 100, or 200 test compounds can be screened for specific binding to INTSIG. Examples of test compounds can include antibodies, anticalins, oligonucleotides, proteins (e.g., ligands or receptors), or small molecules.

In related embodiments, variants of INTSIG can be used to screen for binding of test compounds, such as antibodies, to INTSIG, a variant of INTSIG, or a combination of INTSIG and/or one or more variants INTSIG. In an embodiment, a variant of INTSIG can be used to screen for compounds that bind to a variant of INTSIG, but not to INTSIG having the exact sequence of a sequence of SEQ ID NO:1-45. INTSIG variants used to perform such screening can have a range of about 50% to about 99% sequence identity to INTSIG, with various embodiments having 60%, 70%, 75%, 80%, 85%, 90%, and 95% sequence identity.

In an embodiment, a compound identified in a screen for specific binding to INTSIG can be closely related to the natural ligand of INTSIG, e.g., a ligand or fragment thereof, a natural substrate, a structural or finctional mimetic, or a natural binding partner (Coligan, J. E. et al. (1991) Current Protocols in Immunology 1(2):Chapter 5). In another embodiment, the compound thus identified can be a natural ligand of a receptor INTSIG (Howard, A. D. et al. (2001) Trends Pharmacol. Sci. 22:132-140; Wise, A. et al. (2002) Drug Discovery Today 7:235-246).

In other embodiments, a compound identified in a screen for specific binding to INTSIG can be closely related to the natural receptor to which INTSIG binds, at least a fragment of the receptor, or a fragment of the receptor including all or a portion of the ligand binding site or binding pocket. For example, the compound maybe a receptor for INTSIG which is capable of propagating a signal, or a decoy receptor for INTSIG which is not capable of propagating a signal (Ashkenazi, A. and V. M. Divit (1999) Curr. Opin. Cell Biol. 11:255-260; Mantovani, A. et al. (2001) Trends Immunol. 22:328-336). The compound can be rationally designed using known techniques. Examples of such techniques include those used to construct the compound etanercept UNBREL; Amgen Inc., Thousand Oaks Calif.), which is efficacious for treating rheumatoid arthritis in humans. Etanercept is an engineered p75 tumor necrosis factor (TF) receptor dimer linked to the Fc portion of human IgG₁ (Taylor, P. C. et al. (2001) Curr. Opin. Immunol. 13:611-616).

In one embodiment, two or more antibodies having similar or, alternatively, different specificities can be screened for specific binding to INTSIG, fragments of INTSIG, or variants of INTSIG. The binding specificity of the antibodies thus screened can thereby be selected to identify particular fragments or variants of INTSIG. In one embodiment, an antibody can be selected such that its binding specificity allows for preferential identification of specific fragments or variants of INTSIG. In another embodiment, an antibody can be selected such that its binding specificity allows for preferential diagnosis of a specific disease or condition having increased, decreased, or otherwise abnormal production of INTSIG.

In an embodiment, anticalins can be screened for specific binding to INTSIG, fragments of INTSIG, or variants of INTSIG. Anticalins are ligand-binding proteins that have been constructed based on a lipocalin scaffold (Weiss, G. A. and H. B. Lowman (2000) Chem. Biol. 7:R177-R184; Skerra, A. (2001) J. Biotechnol. 74:257-275). The protein architecture of lipocalins can include a beta-barrel having eight antiparallel beta-strands, which supports four loops at its open end. These loops form the natural ligand-binding site of the lipocalins, a site which can be re-engineered in vitro by amino acid substitutions to impart novel binding specificities. The amino acid substitutions can be made using methods known in the art or described herein, and can include conservative substitutions (e.g., substitutions that do not alter binding specificity) or substitutions that modestly, moderately, or significantly alter binding specificity.

In one embodiment, screening for compounds which specifically bind to, stimulate, or inhibit INTSIG involves producing appropriate cells which express INTSIG, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing INTSIG or cell membrane fractions which contain INTSIG are then contacted with a test compound and binding, stimulation, or inhibition of activity of either INTSIG or the compound is analyzed.

An assay may simply test binding of a test compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. For example, the assay may comprise the steps of combining at least one test compound with INTSIG, either in solution or affixed to a solid support, and detecting the binding of INTSIG to the compound. Alternatively, the assay may detect or measure binding of a test compound in the presence of a labeled competitor. Additionally, the assay may be carried out using cell-free preparations, chemical libraries, or natural product mixtures, and the test compound(s) maybe free in solution or affixed to a solid support.

An assay can be used to assess the ability of a compound to bind to its natural ligand and/or to inhibit the binding of its natural ligand to its natural receptors. Examples of such assays include radio-labeling assays such as those described in U.S. Pat. No. 5,914,236 and U.S. Pat. No. 6,372,724. In a related embodiment, one or more amino acid substitutions can be introduced into a polypeptide compound (such as a receptor) to improve or alter its ability to bind to its natural ligands (Matthews, D. J. and J. A. Wells. (1994) Chem. Biol. 1:25-30). In another related embodiment, one or more amino acid substitutions can be introduced into a polypeptide compound (such as a ligand) to improve or alter its ability to bind to its natural receptors (Cunningham, B. C. and J. A. Wells (1991) Proc. Natl. Acad. Sci. USA 88:3407-3411; Lowman, H. B. et al. (1991) J. Biol. Chem. 266:10982-10988).

INTSIG, fragments of INTSIG, or variants of INTSIG may be used to screen for compounds that modulate the activity of INTSIG. Such compounds may include agonists, antagonists, or partial or inverse agonists. In one embodiment, an assay is performed under conditions permissive for INTSIG activity, wherein INTSIG is combined with at least one test compound, and the activity of INTSIG in the presence of a test compound is compared with the activity of INTSIG in the absence of the test compound. A change in the activity of INTSIG in the presence of the test compound is indicative of a compound that modulates the activity of INTSIG. Alternatively, a test compound is combined with an in vitro or cell-free system comprising INTSIG under conditions suitable for INTSIG activity, and the assay is performed. In either of these assays, a test compound which modulates the activity of INTSIG may do so indirectly and need not come in direct contact with the test compound. At least one and up to a plurality of test compounds may be screened.

In another embodiment, polynucleotides encoding INTSIG or their mammalian homologs may be “knocked out” in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease (see, e.g., U.S. Pat. No. 5,175,383 and U.S. Pat. No. 5,767,337). For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M. R. (1989) Science 244:1288-1292). The vector integrates into die corresponding region of the host genome by homologous recombination Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J. D. (1996) Clin. Invest 97:1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.

Polynucleotides encoding INTSIG may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J. A. et al (1998) Science 282:1145-1147).

Polynucleotides encoding INTSIG can also be used to create “knockin” humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of a polynucleotide encoding INTSIG is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress INTSIG, e.g., by secreting INTSIG in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

Therapeutics

Chemical and structural similarity, e.g., in the context of sequences and motifs, exists between regions of INTSIG and intracellular signaling molecules. In addition, examples of tissues expressing INTSIG can be found in Table 6 and can also be found in Example M. In addition, the expression of GTPA is closely associated with [From PF-1145 P normal skin, testicular, endometrial tissues and diseased lung tissues From PF-1 160 brain tumor, dentate nucleus, and smooth muscle cell tissues, PF-1162 small intestine and testicular tumor tissues, from PF-1170 P sacral bone tumor, amygdala and entorhinal cortex, diseased gallbladder, and small intestine tissues, from PF-11 87 diseased brain tissue, and normal tissues such as striatum, globus pallidus, posterior putamen, breast, smooth muscle, spleen, testicular, and thymus tissues. Therefore, INTSIG appears to play a role in cell proliferative, endocrine, autoimmune/inflammatory, neurological, gastrointestinal, reproductive, developmental, and vesicle trafficking disorders. In the treatment of disorders associated with increased INTSIG expression or activity, it is desirable to decrease the expression or activity of INTSIG. In the treatment of disorders associated with decreased INTSIG expression or activity, it is desirable to increase the expression or activity of INTSIG.

Therefore, in one embodiment, INTSIG or a fragrant or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of INTSIG. Examples of such disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an endocrine disorder such as a disorder of the hypothalamus and pituitary resulting from a lesion such as a primary brain tumor, adenoma, infarction associated with pregnancy, hypophysectomy, aneurysm, vascular malformation, thrombosis, infection, immunological disorder, and a complication due to head trauma; a disorder associated with hypopituitarism including hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism; a disorder associated with hyperpituitarism including acromegaly, giantism, and syndrome of inappropriate antidiuretic hormone secretion (SIADH); a disorder associated with hypothyroidism including goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism; a disorder associated with hyperthyroidism including thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease; a disorder associated with hyperparathyroidism including Conn disease (chronic hypercalemia); a pancreatic disorder such as Type I or Type II diabetes mellitus and associated complications; a disorder associated with the adrenals such as hyperplasia, carcinoma, or adenoma of the adrenal cortex, hypertension associated with alkalosis, amyloidosis, hypokalemia, Cushing's disease, Liddle's syndrome, and Arnold-Healy-Gordon syndrome, pheochromocytoma tumors, and Addison's disease; a disorder associated with gonadal steroid hormones such as: in women, abnormal prolactin production, infertility, endometriosis, perturbations of the menstrual cycle, polycystic ovarian disease, hyperprolactinemia, isolated gonadotropin deficiency, amenorrhea, galactorrhea, hermaphroditism, hirsutism and virilization, breast cancer, and, in post-menopausal women, osteoporosis; and, in men, Leydig cell deficiency, male climacteric phase, and germinal cell aplasia, a hypergonadal disorder associated with a Leydig cell tumor, androgen resistance associated with absence of androgen receptors, syndrome of 5 α-reductase, and gynecomastia; an autoimmune/inflammatory disorder such as acquired imnmunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erylhroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal and helminthic infections, and trauma; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial tbrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, aiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia; a gastrointestinal disorder such as dysphagia, peptic esophagitis, esophageal spasm, esophageal stricture, esophageal carcinoma, dyspepsia, indigestion, gastritis, gastric carcinoma, anorexia, nausea, emesis, gastroparesis, antral or pyloric edema, abdominal angina, pyrosis, gastroenteritis, intestinal obstruction, infections of the intestinal tract, peptic ulcer, cholelithiasis, cholecystitis, cholestasis, pancreatitis, pancreatic carcinoma, biliary tract disease, hepatitis, hyperbilirubinemia, cirrhosis, passive congestion of the liver, hepatoma, infectious colitis, ulcerative colitis, ulcerative proctitis, Crohn's disease, Whipple's disease, Mallory-Weiss syndrome, colonic carcinoma, colonic obstruction, irritable bowel syndrome, short bowel syndrome, diarrhea, constipation, gastrointestinal hemorrhage, acquired immunodeficiency syndrome (AIDS) enteropathy, jaundice, hepatic encephalopathy, hepatorenal syndrome, hepatic steatosis, hemochromatosis, Wilson's disease, alpha₁-antitrypsin deficiency, Reye's syndrome, primary sclerosing cholangitis, liver infarction, portal vein obstruction and thrombosis, centrilobular necrosis, peliosis hepatis, hepatic vein thrombosis, veno-occlusive disease, preeclampsia, eclampsia, acute fatty liver of pregnancy, intrahepatic cholestasis of pregnancy, and hepatic tumors including nodular hyperplasias, adenomas, and carcinomas; a reproductive disorder such as a disorder of prolactin production, infertility, including tubal disease, ovulatory defects, endometriosis, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, ectopic pregnancy, teratogenesis, cancer of the breast, fibrocystic breast disease, galactorrhea, a disruption of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, gynecomastia, hypergonadotropic and hypogonadotropic hypogonadism, pseudohermaphroditism, azoospermia, premature ovarian failure, acrosin deficiency, delayed puperty, retrograde ejaculation and anejaculation, haemangioblastomas, cystsphaeochromocytomas, paraganglioma, cystadenomas of the epididymis, and endolymphatic sac tumours; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; and a vesicle trafficking disorder such as cystic fibrosis, glucose-galactose malabsorption syndrome, hypercholesterolemia, diabetes mellitus, diabetes insipidus, hyper- and hypoglycemia, Grave's disease, goiter, Cushing's disease, and Addison's disease, gastrointestinal disorders including ulcerative colitis, gastric and duodenal ulcers, other conditions associated with abnormal vesicle trafficking, including acquired inmunodeficiency syndrome (AIDS), allergies including hay fever, asthma, and urticaria (hives), autoimmune hemolytic anemia, proliferative glomerulonephritis, inflammatory bowel disease, multiple sclerosis, myasthenia gravis, rheumatoid and osteoarthritis, scleroderma, Chediak-Higashi and Sjogren's syndromes, systemic lupus erythematosus, toxic shock syndrome, and traumatic tissue damage.

In another embodiment, a vector capable of expressing INTSIG or a fragment or derivative thereof maybe administered to a subject to treat or prevent a disorder associated with decreased expression or activity of INTSIG including, but not limited to, those described above.

In a further embodiment, a composition comprising a substantially purified INTSIG in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of INTSIG including, but not limited to, those provided above.

In still another embodiment, an agonist which modulates the activity of INTSIG maybe administered to a subject to treat or prevent a disorder associated with decreased expression or activity of INTSIG including, but not limited to, those listed above.

In a further embodiment, an antagonist of INTSIG may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of INTSIG. Examples of such disorders include, but are not limited to, those cell proliferative, endocrine, autoimmune/inflammatory, neurological, gastrointestinal, reproductive, developmental, and vesicle trafficking disorders described above. In one aspect, an antibody which specifically binds INTSIG maybe used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissues which express INTSIG.

In an additional embodiment, a vector expressing the complement of the polynucleotide encoding INTSIG may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of INTSIG including, but not limited to, those described above.

In other embodiments, any protein, agonist, antagonist, antibody, complementary sequence, or vector embodiments may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.

An antagonist of INTSIG may be produced using methods which are generally known in the art. In particular, purified INTSIG may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind INTSIG. Antibodies to INTSIG may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are generally preferred for therapeutic use. Single chain antibodies (e.g., from camels or llamas) may be potent enzyme inhibitors and may have advantages in the design of peptide minetics, and in the development of immuno-adsorbents and biosensors (Muyldermans, S. (2001) J. Biotechnol. 74:277-302).

For the production of antibodies, various hosts including goats, rabbits, rats, mice, camels, dromedaries, llamas, humans, and others may be immunized by injection with INTSIG or with any fragment or oligopeptide thereof which has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacili Calmette-Guerin) and Corynebacterium parvum are especially preferable.

It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to INTSIG have an amino acid sequence consisting of at least about 5 amino acids, and generally will consist of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein. Short stretches of INTSIG amino acids may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.

Monoclonal antibodies to INTSIG maybe prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kohler, G. et al. (1975) Nature 256:495-497; Kozbor, D. et al (1985) J. Immunol. Methods 81:3142; Cote, R. J. et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030; Cole, S. P. et al. (1984) Mol. Cell Biol. 62:109-120).

In addition, techniques developed for the production of “chimeric antibodies,” such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used (Morrison, S. L. et al. (1984) Proc. Natl. Acad. Sci. USA 81:6851-6855; Neuberger, M. S. et al. (1984) Nature 312:604-608; Takeda, S. et al. (1985) Nature 314:452-454). Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce INTSIG-specific single chain antibodies. Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries (Burton, D. R (1991) Proc. Natl Acad. Sci. USA 88:10134-10137).

Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA 86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299).

Antibody fragments which contain specific binding sites for INTSIG may also be generated. For example, such fragments include, but are not limited to, F(ab′)₂ fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab′)₂ fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse, W. D. et al. (1989) Science 246:1275-1281).

Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between INTSIG and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering INTSIG epitopes is generally used, but a competitive binding assay may also be employed (Pound, supra).

Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for INTSIG. Affinity is expressed as an association constant, K_(a), which is defined as the molar concentration of INTSIG-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions. The K_(a) determined for a preparation of polyclonal antibodies, which are heterogeneous in their affinities for multiple INTSIG epitopes, represents the average affinity, or avidity, of the antibodies for INTSIG. The K_(a) determined for a preparation of monoclonal antibodies, which are monospecific for a particular INTSIG epitope, represents a true measure of affinity. High-affinity antibody preparations with K_(a) ranging from about 10⁹ to 10¹² L/mole are preferred for use in immunoassays in which the INTSIG-antibody complex must withstand rigorous manipulations. Low-affinity antibody preparations with K_(a) ranging from about 10⁶ to 10⁷ L/mole are preferred for use in immunopurification and similar procedures which ultimately require dissociation of INTSIG, preferably in active form, from the antibody (Catty, D. (1988) Antibodies, Volume I: A Practical Approach, IRL Press, Washington D.C.; Liddell, J. E. and A. Cryer (1991) A Practical Guide to Monoclonal Antibodies, John Wiley & Sons, New York N.Y.).

The titer and avidity of polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparations for certain downstream applications. For example, a polyclonal antibody preparation containing at least 1-2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml, is generally employed in procedures requiring precipitation of INTSIG-antibody complexes. Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available (Catty, supra; Coligan et al., supra).

In another embodiment of the invention, polynucleotides encoding INTSIG, or any fragment or complement thereof, may be used for therapeutic purposes. In one aspect, modifications of gene expression can be achieved by designing complementary sequences or antisense molecules (DNA, RNA, PNA, or modified oligonucleotides) to the coding or regulatory regions of the gene encoding INTSIG. Such technology is well known in the art, and antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding INTSIG (Agrawal, S., ed. (1996) Antisense Theraoeutics, Humana Press, Totawa N.J.).

In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein (Slater, J. E. et al. (1998) J. Allergy Clin. Immunol. 102:469-475; Scanlon, K. J. et al. (1995) 9:1288-1296). Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors (Miller, A. D. (1990) Blood 76:271; Ausubel et al., supra; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63:323-347). Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art (Rossi, J. J. (1995) Br. Med. Bull. 51:217-225; Boado, R. J. et al. (1998) J. Pharm. Sci. 87:1308-1315; Morris, M. C. et al. (1997) Nucleic Acids Res. 25:2730-2736).

In another embodiment of the invention, polynucleotides encoding INTSIG may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al. (1995) Science 270:475-480; Bordignon, C. et al (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207-216; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R. G. et al. (1995) Hum Gene Therapy 6:667-703), thalassamias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal. R. G. (1995) Science 270:404-410; Verma, I. M. and N. Somia (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl Acad. Sci. USA 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as Plasmodium falciparum and Trypazosoma cruzi). In the case where a genetic deficiency in INTSIG expression or regulation causes disease, the expression of INTSIG from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.

In a further embodiment of the invention, diseases or disorders caused by deficiencies in INTSIG are treated by constructing mammalian expression vectors encoding INTSIG and introducing these vectors by mechanical means into INTSIG-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R. A. and W. P. Anderson (1993) Annu. Rev. Biochem. 62:191-217; Ivics, Z. (1997) Cell 91:501-510; Boulay, J.-L. and H. Récipon (1998) Curr. Opin. Biotechnol. 9:445-450).

Expression vectors that may be effective for the expression of INTSIG include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX, PCR2-TOPOTA vectors (Invitrogen, Carlsbad Calif.), PCMV-SCRIPT, PCMV-TAG, PEGSHIPERV (Stratagene, La Jolla Calif.), and PTET-OFF, PTET-ON, PTRE2, NVM2-LUC, PTK-HYG (Clontech, Palo Alto Calif.). INTSIG maybe expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter (e.g., the tetracycline-regulated promoter (Gossen, M. and H Bujard (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Gossen, M. et al. (1995) Science 268:1766-1769; Rossi, F. M. V. and R. M. Blau (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen)); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, P. M. V. and H. M. Blau, supra)), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding INTSIG from a normal individual.

Commercially available liposome transformation kits (e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F. L. and A. J. Eb (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.

In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to INTSIG expression are treated by constructing a retrovirus vector consisting of (i) the polynucleotide encoding INTSIG under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. USA 92:6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M. A. et al. (1987) J. Virol. 61:1639-1646; Adam, M. A. and A. D. Miller (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Pat. No. 5,910,434 to Rigg (“Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant”) discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4⁺T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al (1997) J. Virol. 71:7020-7029; Bauer, G. et al (1997) Blood 89:2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al (1998) Proc. Natl. Acad. Sci. USA 95:1201-1206; Su, L. (1997) Blood 89:2283-2290).

In an embodiment, an adenovirus-based gene therapy delivery system is used to deliver polynucleotides encoding INTSIG to cells which have one or more genetic abnormalities with respect to the expression of INTSIG. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M. E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Pat. No. 5,707,618 to Armentano (“Adenoviras vectors for gene therapy”), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P. A. et al. (1999; Annu. Rev. Nutr. 19:511-544) and Verma, I. M. and N. Somia (1997; Nature 18:389:239-242).

In another embodiment, a herpes-based, gene therapy delivery system is used to deliver polynucleotides encoding INTSIG to target cells which have one or more genetic abnormalities with respect to the expression of INTSIG. The use of herpes simplex virus (HSV)-based vectors may be especially valuable for introducing INTSIG to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res. 169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Pat. No. 5,804,413 to DeLuca (“Herpes simplex virus strains for gene transfer” ), which is hereby incorporated by reference. U.S. Patent No. 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. (1999; J. Virol. 73:519-532) and Xu, H. et al. (1994; Dev. Biol. 163:152-161). The manipulation of cloned herpes virus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpes virus genomes, the growth and propagation of herpes virus, and the infection of cells with herpes virus are techniques well known to those of ordinary skill in the art.

In another embodiment, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver polynucleotides encoding INTSIG to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, R and K.-J. Li (1998) Curr. Opin. Biotechnol. 9:464-469). During alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenonic RNA replicates to higher levels than the full length genomnic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting the coding sequence for INTSIG into the alphavirus genome in place of the capsid-coding region results in the production of a large number of INTSIG-coding RNAs and the synthesis of high levels of INTSIG in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S. A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of INTSIG into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.

Oligonucleotides derived from the transcription initiation site, e.g., between about positions −10 and +10 from the start site, may also be employed to inhibit gene expression. Similarly, inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature (Gee, J. E. et al (1994) in Huber, B. E. and B. I. Carr, Molecular and Immunologic Approaches, Futura Publishing, Mt. Kisco N.Y., pp. 163-177). A complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. For example, engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of RNA molecules encoding INTSIG.

Specific ribozyme cleavage sites within any potential RNA target are initially identified by canning the target molecule for ribozyme cleavage sites, including the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, maybe evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.

Complementary ribonucleic acid molecules and ribozymes may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules maybe generated by in vitro and in vivo transcription of DNA molecules encoding INTSIG. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as 17 or SP6. Alternatively, these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.

RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3 ′ ends of the molecule, or the use of phosphorothioate or 2′O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.

An additional embodiment of the invention encompasses a method for screening for a compound which is effective in altering expression of a polynucleotide encoding INTSIG. Compounds which may be effective in altering expression of a specific polynucleotide may include, but are not limited to, oligonucleotides, antisense oligonucleotides, triple helix-forming oligonucleotides, transcription factors and other polypeptide transcriptional regulators, and non-macromolecular chemical entities which are capable of interacting with specific polynucleotide sequences. Effective compounds may alter polynucleotide expression by acting as either inhibitors or promoters of polynucleotide expression. Thus, in the treatment of disorders associated with increased INTSIG expression or activity, a compound which specifically inhibits expression of the polynucleotide encoding INTSIG may be therapeutically useful, and in the treatment of disorders associated with decreased INTSIG expression or activity, a compound which specifically promotes expression of the polynucleotide encoding INTSIG may be therapeutically useful.

At least one, and up to a plurality, of test compounds may be screened for effectiveness in altering expression of a specific polynucleotide. A test compound may be obtained by any method commonly known in the art, including chemical modification of a compound known to be effective in altering polynucleotide expression; selection from an existing, commercially-available or proprietary library of naturally-occurring or non-natural chemical compounds; rational design of a compound based on chemical and/or structural properties of the target polynucleotide; and selection from a library of chemical compounds created combinatorially or randomly. A sample comprising a polynucleotide encoding INTSIG is exposed to at least one test compound thus obtained. The sample may comprise, for example, an intact or permeabilized cell, or an in vitro cell-free or reconstituted biochemical system. Alterations in the expression of a polynucleotide encoding INTSIG are assayed by any method commonly known in the art. Typically, the expression of a specific nucleotide is detected by hybridization with a probe having a nucleotide sequence complementary to the sequence of the polynucleotide encoding INTSIG. The amount of hybridization may be quantified, thus forming the basis for a comparison of the expression of the polynucleotide both with and without exposure to one or more test compounds. Detection of a change in the expression of a polynucleotide exposed to a test compound indicates that the test compound is effective in altering the expression of the polynucleotide. A screen for a compound effective in altering expression of a specific polynucleotide can be carried out, for example, using a Schizosaccharomyces pombe gene expression system (Atkins, D. et al. (1999) U.S. Pat. No. 5,932,435; Arndt, G. M. et al. (2000) Nucleic Acids Res. 28:E15) or a human cell line such as HeLa cell (Clarke, M. L. et al. (2000) Biochem. Biophys. Res. Commun. 268:8-13). A particular embodiment of the present invention involves screening a combinatorial library of oligonucleotides (such as deoxyribonucleotides, ribonucleotides, peptide nucleic acids, and modified oligonucleotides) for antisense activity against a specific polynucleotide sequence (Bruice, T. W. et al. (1997) U.S. Pat. No. 5,686,242; Bruice, T. W. et al. (2000) U.S. Pat. No. 6,022,691).

Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors maybe introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art (Goldman, C. K et al. (1997) Nat Biotechnol. 15:462-466).

Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as humans, dogs, cats, cows, horses, rabbits, and monkeys.

An additional embodiment of the invention relates to the administration of a composition which generally comprises an active ingredient formulated with a pharmaceutically acceptable excipient. Excipients may include, for example, sugars, starches, celluloses, gums, and proteins. Various formulations are commonly known and are thoroughly discussed in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing, Easton Pa.). Such compositions may consist of INTSIG, antibodies to INTSIG, and mimetics, agonists, antagonists, or inhibitors of INTSIG.

The compositions utilized in this invention maybe administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, pulmonary, transdermal, subcutaneous, intraperitoneal intranasal, enteral, topical, sublingual, or rectal means.

Compositions for pulmonary administration may be prepared in liquid or dry powder form. These compositions are generally aerosolized immediately prior to inhalation by the patient. In the case of small molecules (e.g. traditional low molecular weight organic drugs), aerosol delivery of fast-acting formulations is well-known in the art. In the case of macromolecules (e.g. larger peptides and proteins), recent developments in the field of pulmonary delivery via the alveolar region of the lung have enabled the practical delivery of drugs such as insulin to blood circulation (see, e.g., Patton, J. S. et al., U.S. Pat. No. 5,997,848). Pulmonary delivery has the advantage of administration without needle injection, and obviates the need for potentially toxic penetration enhancers.

Compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose. The determination of an effective dose is well within the capability of those skilled in the art.

Specialized forms of compositions may be prepared for direct intracellular delivery of macromolecules comprising INTSIG or fragments thereof. For example, liposome preparations containing a cell-impermeable macromolecule may promote cell fusion and intracellular delivery of the macromolecule. Alternatively, INTSIG or a fragment thereof may be joined to a short cationic N-terminal portion from the HIV Tat-1 protein. Fusion proteins thus generated have been found to transduce into the cells of all tissues, including the brain, in a mouse model system (Schwarze, S. R. et al. (1999) Science 285:1569-1572).

For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models such as mice, rats, rabbits, dogs, monkeys, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

A therapeutically effective dose refers to that amount of active ingredient, for example INTSIG or fragments thereof, antibodies of INTSIG, and agonists, antagonists or inhibitors of INTSIG, S which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED₅₀ (the dose therapeutically effective in 50% of the population) or LD₅₀ (the dose lethal to 50% of the population) statistics. The dose ratio of toxic to therapeutic effects is the therapeutic index, which can be expressed as the LD₅/ED₅ ratio. Compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that includes the ED₅₀ with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration.

The exact dosage will be determined by the practitioner, in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.

Normal dosage amounts may vary from about 0.1 μg to 100,000 μg, up to a total dose of about 1 gram, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

Diagnostics

In another embodiment, antibodies which specifically bind INTSIG may be used for the diagnosis of disorders characterized by expression of INTSIG, or in assays to monitor patients being treated with INTSIG or agonists, antagonists, or inhibitors of INTSIG. Antibodies useful for diagnostic purposes may be prepared in the same manner as described above for therapeutics. Diagnostic assays for INTSIG include methods which utilize the antibody and a label to detect INTSIG in human body fluids or in extracts of cells or tissues. The antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule. A wide variety of reporter molecules, several of which are described above, are known in the art and maybe used.

A variety of protocols for measuring INTSIG, including ELISAs, RIAs, and FACS, are known in the art and provide a basis for diagnosing altered or abnormal levels of INTSIG expression. Normal or standard values for INTSIG expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, for example, human subjects, with antibodies to INTSIG under conditions suitable for complex formation. The amount of standard complex formation may be quantitated by various methods, such as photometric means. Quantities of INTSIG expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease.

In another embodiment of the invention, polynucleotides encoding INTSIG may be used for diagnostic purposes. The polynucleotides which may be used include oligonucleotides, complementary RNA and DNA molecules, and PNAs. The polynucleotides may be used to detect and quantify gene expression in biopsied tissues in which expression of INTSIG may be correlated with disease. The diagnostic assay maybe used to determine absence, presence, and excess expression of INTSIG, and to monitor regulation of INTSIG levels during therapeutic intervention.

In one aspect, hybridization with PCR probes which are capable of detecting polynucleotides, including genomic sequences, encoding INTSIG or closely related molecules may be used to identify nucleic acid sequences which encode INTSIG. The specificity of the probe, whether it is made from a highly specific region, e.g., the 5′regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification will determine whether the probe identifies only naturally occurring sequences encoding INTSIG, allelic variants, or related sequences.

Probes may also be used for the detection of related sequences, and may have at least 50% sequence identity to any of the INTSIG encoding sequences. The hybridization probes of the subject invention may be DNA or RNA and maybe derived from the sequence of SEQ ID NO:46-90 or from genomic sequences including promoters, enhancers, and introns of the INTSIG gene.

Means for producing specific hybridization probes for polynucleotides encoding INTSIG include the cloning of polynucleotides encoding INTSIG or INTSIG derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides. Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as ³⁵P or ³⁵S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.

Polynucleotides encoding INTSIG maybe used for the diagnosis of disorders associated with expression of INTSIG. Examples of such disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an endocrine disorder such as a disorder of the hypothalamus and pituitary resulting from a lesion such as a primary brain tumor, adenoma, infarction associated with pregnancy, hypophysectomy, aneurysm, vascular malformation, thrombosis, infection, immunological disorder, and a complication due to head trauma; a disorder associated with hypopituitarism including hypogonadism, Sheehan syndrome, diabetes insipidus, Kalman's disease, Hand-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism; a disorder associated with hyperpituitarism including acromegaly, giantism, and syndrome of inappropriate antidiuretic hormone secretion (SIADH); a disorder associated with hypothyroidism including goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism; a disorder associated with hyperthyroidism including thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease; a disorder associated with hyperparathyroidism including Conn disease (chronic hypercalemia); a pancreatic disorder such as Type I or Type II diabetes mellitus and associated complications; a disorder associated with the adrenals such as hyperplasia, carcinoma, or adenoma of the adrenal cortex, hypertension associated with alkalosis, amyloidosis, hypokalemia, Cushing's disease, Liddle's syndrome, and Arnold-Healy-Gordon syndrome, pheochromocytoma tumors, and Addison's disease; a disorder associated with gonadal steroid hormones such as: in women, abnormal prolactin production, infertility, endometriosis, perturbations of the menstrual cycle, polycystic ovarian disease, hyperprolactinemia, isolated gonadotropin deficiency, amenorrhea, galactorhea, hermaphroditism, hirsutism and virilization, breast cancer, and, in post-menopausal women, osteoporosis; and, in men, Leydig cell deficiency, male climacteric phase, and germinal cell aplasia, a hypergonadal disorder associated with a Leydig cell tumor, androgen resistance associated with absence of androgen receptors, syndrome of 5 α-reductase, and gynecomastia; an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erydlema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retintis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia; a gastrointestinal disorder such as dysphagia, peptic esophagitis, esophageal spasm, esophageal stricture, esophageal carcinoma, dyspepsia, indigestion, gastritis, gastric carcinoma, anorexia, nausea, emesis, gastroparesis, antral or pyloric edema, abdominal angina, pyrosis, gastroenteritis, intestinal obstruction, infections of the intestinal tract, peptic ulcer, cholelithiasis, cholecystitis, cholestasis, pancreatitis, pancreatic carcinoma, biliary tract disease, hepatitis, hyperbilirubinemia, cirrhosis, passive congestion of the liver, hepatoma, infectious colitis, ulcerative colitis, ulcerative proctitis, Crohn's disease, Whipple's disease, Mallory-Weiss syndrome, colonic carcinoma, colonic obstruction, irritable bowel syndrome, short bowel syndrome, diarrhea, constipation, gastrointestinal hemorrhage, acquired immunodeficiency syndrome (AIDS) enteropathy, jaundice, hepatic encephalopathy, hepatorenal syndrome, hepatic steatosis, hemochromatosis, Wilson's disease, alpha₁-antitrypsin deficiency, Reye's syndrome, primary sclerosing cholangitis, liver infarction, portal vein obstruction and thrombosis, centrilobular necrosis, peliosis hepatis, hepatic vein thrombosis, veno-occlusive disease, preeclampsia, eclampsia, acute fatty liver of pregnancy, intrahepatic cholestasis of pregnancy, and hepatic tumors including nodular hyperplasias, adenomas, and carcinomas; a reproductive disorder such as a disorder of prolactin production, infertility, including tubal disease, ovulatory defects, endometriosis, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, ectopic pregnancy, teratogenesis, cancer of the breast, fibrocystic breast disease, galactorrhea, a disruption of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, gynecomastia, hypergonadotropic and hypogonadotropic hypogonadism, pseudohermaphroditism, azoosperria, premature ovarian failure, acrosin deficiency, delayed puperty, retrograde ejaculation and anejaculation, haemangioblastomas, cystsphaeochromocytomas, paraganglioma, cystadenomas of the epididymis, and endolymphatic sac tumours; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; and a vesicle trafficking disorder such as cystic fibrosis, glucose-galactose malabsorption syndrome, hypercholesterolemia, diabetes mellitus, diabetes insipidus, hyper- and hypoglycemia, Grave's disease, goiter, Cushing's disease, and Addison's disease, gastrointestinal disorders including ulcerative colitis, gastric and duodenal ulcers, other conditions associated with abnormal vesicle trafficking, including acquired immunodeficiency syndrome (AIDS), allergies including hay fever, asthma, and urticaria (hives), autoimmune hemolytic anemia, proliferative glomerulonephritis, inflammatory bowel disease, multiple sclerosis, myasthenia gravis, rheumatoid and osteoarthritis, scleroderma, Chediak-Higashi and Sjogren's syndromes, systemic lupus erythematosus, toxic shock syndrome, and traumatic tissue damage. Polynucleotides encoding INTSIG may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies; in dipstick, pin, and multiformat ELISA-like assays; and in microarrays utilizing fluids or tissues from patients to detect altered INTSIG expression. Such qualitative or quantitative methods are well known in the art.

In a particular aspect, polynucleotides encoding INTSIG may be used in assays that detect the presence of associated disorders, particularly those mentioned above. Polynucleotides complementary to sequences encoding INTSIG may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantified and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of polynucleotides encoding INTSIG in the sample indicates the presence of the associated disorder. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.

In order to provide a basis for the diagnosis of a disorder associated with expression of INTSIG, a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding INTSIG, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.

Once the presence of a disorder is established and a treatment protocol is initiated, hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject The results obtained from successive assays maybe used to show the efficacy of treatment over a period ranging from several days to months.

With respect to cancer, the presence of an abnormal amount of transcript (either under- or overexpressed) in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier, thereby preventing the development or further progression of the cancer.

Additional diagnostic uses for oligonucleotides designed from the sequences encoding INTSIG may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced in vitro. Oligomers will preferably contain a fragment of a polynucleotide encoding INTSIG, or a fragment of a polynucleotide complementary to the polynucleotide encoding INTSIG, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantification of closely related DNA or RNA sequences.

In a particular aspect, oligonucleotide primers derived from polynucleotides encoding INTSIG may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from polynucleotides encoding INTSIG are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymorphisms by comparing the sequence of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs maybe detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego Calif.).

SNPs may be used to study the genetic basis of human disease. For example, at least 16 common SNPs have been associated with non-insulin-dependent diabetes mellitus. SNPs are also useful for examining differences in disease outcomes in monogenic disorders, such as cystic fibrosis, sickle cell anemia, or chronic granulomatous disease. For example, variants in the mannose-binding lectin, MBL2, have been shown to be correlated with deleterious pulmonary outcomes in cystic fibrosis. SNPs also have utility in pharmacogenomics, the identification of genetic variants that influence a patient's response to a drug, such as life-threatening toxicity. For example, a variation in N-acetyl transferase is associated with a high incidence of peripheral neuropathy in response to the anti-tuberculosis drug isoniazid, while a variation in the core promoter of the ALOX5 gene results in diminished clinical response to treatment with an anti-asthma drug that targets the 5-lipoxygenase pathway. Analysis of the distribution of SNPs in different populations is useful for investigating genetic drift, mutation, recombination, and selection, as well as for tracing the origins of populations and their migrations (Taylor, J. G. et al. (2001) Trends Mol. Med. 7:507-512; Kwok, P.-Y. and Z. Gu (1999) Mol. Med. Today 5:538-543; Nowotny, P. et al. (2001) Curr. Opin. Neurobiol. 11:637-641).

Methods which may also be used to quantify the expression of INTSIG include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves (Melby, P. C. et al (1993) J. Immunol. Methods 159:235-244; Duplaa, C. et al. (1993) Anal. Biochem. 212:229-236). The speed of quantitation of multiple samples maybe accelerated by running the assay in a high-throughput format where the oligomer or polynucleotide of interest is presented in various dilutions and a spectrophotometric or calorimetric response gives rapid quantitation.

In further embodiments, oligonucleotides or longer fragments derived from any of the polynucleotides described herein may be used as elements on a microarray. The microarray can be used in transcript imaging techniques which monitor the relative expression levels of large numbers of genes simultaneously as described below. The microarray may also be used to identify genetic variants, mutations, and polymorphisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, to monitor progression/regression of disease as a function of gene expression, and to develop and monitor the activities of therapeutic agents in the treatment of disease. In particular, this information may be used to develop a pharmacogenomic profile of a patient in order to select the most appropriate and effective treatment regimen for that patient For example, therapeutic agents which are highly effective and display the fewest side effects may be selected for a patient based on his/her pharmacogenomic profile.

In another embodiment, INTSIG, fragments of INTSIG, or antibodies specific for INTSIG may be used as elements on a microarray. The microarray may be used to monitor or measure protein-protein interactions, drug-target interactions, and gene expression profiles, as described above.

A particular embodiment relates to the use of the polynucleotides of the present invention to generate a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time (Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No.5,840,484; hereby expressly incorporated by reference herein). Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene activity.

Transcript images maybe generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect gene expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.

Transcript images which profile the expression of the polynucleotides of the present invention may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153-159; Steiner, S. and N. L. Anderson (2000) Toxicol. Lett. 112-113:467-471). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity (see, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released Feb. 29, 2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm). Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

In an embodiment, the toxicity of a test compound can be assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.

Another embodiment relates to the use of the polypeptides disclosed herein to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enyymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of interest In some cases, further sequence data may be obtained for definitive protein identification.

A proteomic profile may also be generated using antibodies specific for INTSIG to quantify the levels of INTSIG expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and S detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103-111; Mendoze, L. G. et al. (1999) Biotechniques 27:778-788). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.

Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and J. Seilhamer (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reliable and informative in such cases.

In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the polypeptides of the present invention.

In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the polypeptides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.

Microarrays may be prepared, used, and analyzed using methods known in the art (Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon, D. et al (1995) PCT application WO95/35505; Heller, R. A. et al (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; Heller, M. J. et al. (1997) U.S. Pat. No. 5,605,662). Various types of microarrays are well known and thoroughly described in Schena, M., ed. (1999; DNA Microarrays: A Practical Approach, Oxford University Press, London).

In another embodiment of the invention, nucleic acid sequences encoding INTSIG may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence. Either coding or noncoding sequences may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries (Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355; Price, C. M. (1993) Blood Rev. 7:127-134; Trask, B. J. (1991) Trends Genet. 7:149-154). Once mapped, the nucleic acid sequences may be used to develop genetic linkage maps, for example, which correlate the inheritance of a disease state with the inheritance of a particular chromosome region or restriction fragment length polymorphism (RFLP) (Lander, E. S. and D. Botstein (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357).

Fluorescent in situ hybridization (FISH) may be correlated with other physical and genetic map data (Heinz-Ulrich, et al. (1995) in Meyers, supra, pp. 965-968). Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site. Correlation between the location of the gene encoding INTSIG on a physical map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder and thus may further positional cloning efforts.

In situ hybridization of chromosomal preparations and physical mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the exact chromosomal locus is not known. This information is valuable to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the gene or genes responsible for a disease or syndrome have been crudely localized by genetic linkage to a particular genomic region, e.g., ataxia-telangiectasia to 11q22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation (Gatti, R. A. et al. (1988) Nature 336:577-580). The nucleotide sequence of the instant invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.

In another embodiment of the invention, INTSIG, its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques. The fragment employed in such screening maybe free in solution, affixed to a solid support, borne on a cell surface, or located intracelularly. The formation of binding complexes between INTSIG and the agent being tested may be measured.

Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest (Geysen, et al (1984) PCT application WO84/03564). In this method, large numbers of different small test compounds are synthesized on a solid substrate. The test compounds are reacted with INTSIG, or fragments thereof, and washed. Bound INTSIG is then detected by methods well known in the art. Purified INTSIG can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.

In another embodiment, one may use competitive drug screening assays in which neutralizing antibodies capable of binding INTSIG specifically compete with a test compound for binding INTSIG. In this manner, antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with INTSIG.

In additional embodiments, the nucleotide sequences which encode INTSIG maybe used in any molecular biologgy techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.

Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

The disclosures of all patents, applications, and publications mentioned above and below, including U.S. Ser. No. 60/313,245, U.S. Ser. No. 60/314,751, U.S. Ser. No. 60/316,752, U.S. Ser. No. 60/316,847, U.S. Ser. No. 60/322,188, U.S. Ser. No. 60/326,390, U.S. Ser. No. 60/328,952, U.S. Ser. No. 60/345,468, and U.S. Ser. No. 60/372,499, are hereby expressly incorporated by reference.

EXAMPLES

I. Construction of cDNA Libraries

Incyte cDNAs were derived from cDNA libraries described in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.) and shown in Table 4, column 3. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Invitrogen), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform RNA was precipitated from the lysates with either isopropanol or sodium acetate and ethanol, or by other routine methods.

Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In some cases, RNA was treated with DNase. For most libraries, poly(A)+ RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN, Chatsworth Calif.), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Austin Tex.).

In some cases, Stratagene was provided with RNA and constructed the corresponding cDNA libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Invitrogen), using the recommended procedures or similar methods known in the art (Ausubel et al., supra, ch. 5). Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Biosciences) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (Invitrogen), PCDNA2.1 plasmid Invitrogen, Carlsbad Calif.), PBK-CMV plasmid (Stratagene), PCR2-TOPOTA plasmid (Invitrogen), PCMV-ICIS plasmid (Stratagene), pIGEN (Incyte Genomics, Palo Alto Calif.), pRARE (Incyte Genomics), or pINCY (Incyte Genomics), or derivatives thereof. Recombinant plasmids were transformed into competent E. coli cells including XL1-Blue, XL1-BlueMRF, or SOLR from Stratagene or DH5α, DH10B, or ElectroMAX DH10B from Invitrogen.

II. Isolation of cDNA Clones

Plasmids obtained as described in Example I were recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids were purified using at least one of the following: a Magic or WIZARD Minipreps DNA purification system (Promega); an AGTC Miniprep purification kit (Edge Biosystems, Gaithersburg Md.); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmid, QIAWELL 8 Ultra Plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit from QIAGEN. Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4° C.

Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format (Rao, V. B. (1994) Anal. Biochem. 216:1-14). Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Eugene Oreg.) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

III. Sequencing and Analysis

Incyte cDNA recovered in plasmids as described in Example II were sequenced as follows. Sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 (Applied Biosystems) thermal cycler or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific) or the MICROLAB 2200 (Hamilton) liquid transfer system. cDNA sequencing reactions were prepared using reagents provided by Amersham Biosciences or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MMGABACE 1000 DNA sequencing system (Amersham Biosciences); the ABI PRISM 373 or 377 sequencing system (Applied Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (Ausubel et al, supra, ch, 7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.

The polynucleotide sequences derived from Incyte cDNAs were validated by removing vector, linker, and poly(A) sequences and by masking ambiguous bases, using algorithms and programs based on BLAST, dynamic programming, and dinucleotide nearest neighbor analysis. The Incyte cDNA sequences or translations thereof were then queried against a selection of public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases, and BLOCKS, PRINTS, DOMO, PRODOM; PROTEOME databases with sequences from Homo sapiens, Rattus tiorvegicus, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans (Incyte Genomics, Palo Alto Calif.); hidden Markov model (MM)-based protein family databases such as PFAM, INCY, and TTGRPAM (Haft, D. H. et al. (2001) Nucleic Acids Res. 29:41-43); and i-based protein domain databases such as SMART (Schultz, J. et al. (1998) Proc. Natl. Acad. Sci. USA 95:5857-5864; Letunic, L et al. (2002) Nucleic Acids Res. 30:242-244). (HMM is a probabilistic approach which analyzes consensus primary structures of gene families; see, for example, Eddy, S. R. (1996) Curr. Opin. Struct Biol. 6:361-365.) The queries were performed using programs based on BLAST, PASTA, BLIMPS, and HMMER. The Incyte cDNA sequences were assembled to produce full length polynucleotide sequences. Alternatively, GenBank cDNAs, GenBank ESTs, stitched sequences, stretched sequences, or Genscan-predicted coding sequences (see Examples IV and V) were used to extend Incyte cDNA assemblages to full length. Assembly was performed using programs based on Phred, Phrap, and Consed, and cDNA assemblages were screened for open reading frames using programs based on GeneMark, BLAST, and FASTA. The full length polynucleotide sequences were translated to derive the corresponding full length polypeptide sequences. Alternatively, a polypeptide may begin at any of the methionine residues of the full length translated polypeptide. Full length polypeptide sequences were subsequently analyzed by querying against databases such as the GenBank protein databases (genpept), SwissProt, the PROTEOME databases, BLOCKS, PRINTS, DOMO, PRODOM, Prosite, hidden Markov model (H)-based protein family databases such as PFAM, INCY, and TIGRFAM; and HMM-based protein domain databases such as SMART. Pull length polynucleotide sequences are also analyzed using MACDNASIS PRO software (MiraiBio, Alameda Calif.) and LASERGENE software (DNASTAR). Polynucleotide and polypeptide sequence alignments are generated using default parameters specified by the CLUSTAL algorithm as incorporated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences.

Table 7 summarizes the tools, programs, and algorithms used for the analysis and assembly of Incyte cDNA and full length sequences and provides applicable descriptions, references, and threshold parameters. The first column of Table 7 shows the tools, programs, and algorithms used, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score or the lower the probability value, the greater the identity between two sequences).

The programs described above for the assembly and analysis of full length polynucleotide and polypeptide sequences were also used to identify polynucleotide sequence fragments from SEQ ID NO:46-90. Fragments from about 20 to about 4000 nucleotides which are useful in hybridization and amplification technologies are described in Table 4, column 2.

IV. Identification and Editing of Coding Sequences from Genomic DNA

Putative intracellular signaling molecules were initially identified by running the Genscan gene identification program against public genomic sequence databases (e.g., gbpri and gbhtg). Genscan is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms (Burge, C. and S. Karlin (1997) J. Mol Biol. 268:78-94; Burge, C. and S. Karlin (1998) Curr. Opin. Struct. Biol. 8:346-354). The program concatenates predicted exons to form an assembled cDNA sequence extending from a methionine to a stop codon. The output of Genscan is a FASTA database of polynucleotide and polypeptide sequences. The maximum range of sequence for Genscan to analyze at once was set to 30 kb. To determine which of these Genscan predicted cDNA sequences encode intracellular signaling molecules, the encoded polypeptides were analyzed by querying against PFAM models for intracellular signaling molecules. Potential intracellular signaling molecules were also identified by homology to Incyte cDNA sequences that had been annotated as intracellular signaling molecules. These selected Genscan-predicted sequences were then compared by BLAST analysis to the genpept and gbpri public databases. Where necessary, the Genscan-predicted sequences were then edited by comparison to the top BLAST hit from genpept to correct errors in the sequence predicted by Genscan, such as extra or omitted exons. BLAST analysis was also used to find any Incyte cDNA or public cDNA coverage of the Genscan-predicted sequences, thus providing evidence for transcription When Incyte cDNA coverage was available, this information was used to correct or confirm the Genscan predicted sequence. Full length polynucleotide sequences were obtained by assembling Genscan-predicted coding sequences with Incyte cDNA sequences and/or public cDNA sequences using the assembly process described in Example III. Alternatively, full length polynucleotide sequences were derived entirely from edited or unedited Genscan-predicted coding sequences.

V. Assembly of Genomic Sequence Data with cDNA Sequence Data

“Stitched” Sequences

Partial cDNA sequences were extended with exons predicted by the Genscan gene identification program described in Example IV. Partial cDNAs assembled as described in Example III were mapped to genomic DNA and parsed into clusters containing related cDNAs and Genscan exon predictions from one or more genomic sequences. Each cluster was analyzed using an algorithm based on graph theory and dynamic programming to integrate cDNA and genomic information, generating possible splice variants that were subsequently confirmed, edited, or extended to create a full length sequence. Sequence intervals in which the entire length of the interval was present on more than one sequence in the cluster were identified, and intervals thus identified were considered to be equivalent by transitivity. For example, if an interval was present on a cDNA and two genomic sequences, then all three intervals were considered to be equivalent. This process allows unrelated but consecutive genomic sequences to be brought together, bridged by cDNA sequence. Intervals thus identified were then “stitched” together by the stitching algorithm in the order that they appear along their parent sequences to generate the longest possible sequence, as well as sequence variants. Linkages between intervals which proceed along one type of parent sequence (cDNA to cDNA or genomic sequence to genomic sequence) were given preference over linkages which change parent type (cDNA to genomic sequence). The resultant stitched sequences were translated and compared by BLAST analysis to the genpept and gbpri public databases. Incorrect exons predicted by Genscan were corrected by comparison to the top BLAST hit from genpept. Sequences were further extended with additional cDNA sequences, or by inspection of genomic DNA, when necessary.

“Stretched” Sequences

Partial DNA sequences were extended to full length with an algorithm based on BLAST analysis. First, partial cDNAs assembled as described in Example m were queried against public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases using the BLAST program. The nearest GenBank protein homolog was then compared by BLAST analysis to either Incyte cDNA sequences or GenScan exon predicted sequences described in Example IV. A chimeric protein was generated by using the resultant high-scoring segment pairs (HSPs) to map the translated sequences onto the GenBank protein homolog. Insertions or deletions may occur in the chimeric protein with respect to the original GenBank protein homolog. The GenBank protein homolog, the chimeric protein, or both were used as probes to search for homologous genomic sequences from the public human genome databases. Partial DNA sequences were therefore “stretched” or extended by the addition of homologous genomic sequences. The resultant stretched sequences were examined to determine whether it contained a complete gene.

VI. Chromosomal Mapping of INTSIG Encoding Polynucleotides

The sequences which were used to assemble SEQ ID NO:46-90 were compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that matched SEQ ID NO:46-90 were assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as Phrap (Table 7). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Généthon were used to determine if any of the clustered sequences had been previously mapped. Inclusion of a mapped sequence in a cluster resulted in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location.

Map locations are represented by ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Généthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters. Human genome maps and other resources available to the public, such as the NCBI “GeneMap'99” World Wide Web site (http://www.ncbi.nlm.nih gov/genemap/), can be employed to determine if previously identified disease genes map within or in proximity to the intervals indicated above.

VII. Analysis of Polynucleotide Expression

Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound (Sambrook, supra, ch. 7; Ausubel et al, supra, ch. 4).

Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Genomics). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as: $\frac{\text{BLAST~~Score} \times \text{Percent~~Identity}}{5 \times \text{minimum~~\{length(Seq. 1),~~length(Seq.~~2)\}}}$

The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and −4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.

Alternatively, polynucleotides encoding INTSIG are analyzed with respect to the tissue sources from which they were derived. For example, some fall length sequences are assembled, at least in part, with overlapping Incyte cDNA sequences (see Example III). Each cDNA sequence is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following organ/tissue categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract The number of libraries in each category is counted and divided by the total number of libraries across all categories. Similarly, each human tissue is classified into one of the following disease/condition categories: cancer, cell line, developmental, inflammation, neurological, trauma, cardiovascular, pooled, and other, and the number of libraries in each category is counted and divided by the total number of libraries across all categories. The resulting percentages reflect the tissue, and disease-specific expression of cDNA encoding INTSIG. cDNA sequences and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.).

VIII. Extension of INTSIG Encoding Polynucleotides

Full length polynucleotides are produced by extension of an appropriate fragment of the full length molecule using oligonucleotide primers designed from this fragment. One primer was synthesized to initiate 5′ extension of the known fragment, and the other primer was synthesized to initiate 3′ extension of the known fragment The initial primers were designed using OLIGO 4.06 software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations was avoided.

Selected human cDNA libraries were used to extend the sequence. If more than one extension was necessary or desired, additional or nested sets of primers were designed.

High fidelity amplification was obtained by PCR using methods well known in the art PCR was performed in 96-well plates using the PTC-200 thermal cycler (MJ Research, Inc.). The reaction mix contained DNA template, 200 nmol of each primer, reaction buffer containing Mg²⁺, (NH₄)₂SO₄, and 2-mercaptoethanol, Taq DNA polymerase (Amersham Biosciences), ELONGASE enzyme (Invitrogen), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, the parameters for primer pair T7 and SK+ were as follows: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C.

The concentration of DNA in each well was determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v) PICOGREEN; Molecular Probes, Eugene OR) dissolved in 1×TE and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton Mass.), allowing the DNA to bind to the reagent. The plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture was analyzed by electrophoresis on a 1% agarose gel to determine which reactions were successful in extending the sequence.

The extended nucleotides were desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Biosciences). For shotgun sequencing, the digested nucleotides were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and agar digested with Agar ACE (Promega). Extended clones were religated using T4 ligase (New England Biolabs, Beverly Mass.) into pUC 18 vector (Amersham Biosciences), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells were selected on antibiotic-containing media, and individual colonies were picked and cultured overnight at 37° C. in 384-well plates in LB/2× carb liquid media.

The cells were lysed, and DNA was amplified by PCR using Taq DNA polymerase (Amersham Biosciences) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C. DNA was quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the same conditions as described above. Samples were diluted with 20% dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Biosciences) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems).

In like manner, full length polynucleotides are verified using the above procedure or are used to obtain 5′ regulatory sequences using the above procedure along with oligonucleotides designed for such extension, and an appropriate genomic library.

IX. Identification of Single Nucleotide Polymorphisms in INTSIG Encoding Polynucleotides

Common DNA sequence variants known as single nucleotide polymorphisms (SNPs) were identified in SEQ ID NO:46-90 using the LIFESEQ database (Incyte Genomics). Sequences from the same gene were clustered together and assembled as described in Example III, allowing the identification of all sequence variants in the gene. An algorithm consisting of a series of filters was used to distinguish SNPs from other sequence variants. Preliminary filters removed the majority of basecall errors by requiring a minimum Phred quality score of 15, and removed sequence alignment errors and errors resulting from improper trimming of vector sequences, chimeras, and splice variants. An automated procedure of advanced chromosome analysis analysed the original chromatogram files in the vicinity of the putative SNP. Clone error filters used statistically generated algorithms to identify errors introduced during laboratory processing, such as those caused by reverse transcriptase, polymerase, or somatic mutation. Clustering error filters used statistically generated algorithms to identify errors resulting from clustering of close homologs or pseudogenes, or due to contamination by non-human sequences. A final set of filters removed duplicates and SNPs found in immunoglobulins or T-cell receptors.

Certain SNPs were selected for further characterization by mass spectrometry using the high throughput MASSARRAY system (Sequenom, Inc.) to analyze allele frequencies at the SNP sites in four different human populations. The Caucasian population comprised 92 individuals (46 male, 46 female), including 83 from Utah, four French, three Venezualan, and two Amish individuals. The African population comprised 194 individuals (97 male, 97 female), all African Americans. The Hispanic population comprised 324 individuals (162 male, 162 female), all Mexican Hispanic. The Asian population comprised 126 individuals (64 male, 62 female) with a reported parental breakdown of 43% Chinese, 31% Japanese, 13% Korean, 5% Vietnamese, and 8% other Asian. Allele frequencies were first analyzed in the Caucasian population; in some cases those SNPs which showed no allelic variance in this population were not further tested in the other three populations.

X. Labeling and Use of Individual Hybridization Probes

Hybridization probes derived from SEQ ID NO:46-90 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 software (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250 μCi of [γ-³²P] adenosine triphosphate (Amersham Biosciences), and T4 polynucleotide kinase (DuPont NEN, Boston Mass.). The labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine size exclusion dextran bead column (Amersham Biosciences). An aliquot containing 10⁷ counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba I, or Pvu II (DuPont NEN).

The DNA from each digest is fractionated on a 0.7% agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham N.H.). Hybridization is carried out for 16 hours at 40° C. To remove nonspecific signals, blots are sequentially washed at room temperature under conditions of up to, for example, 0.1× saline sodium citrate and 0.5% sodium dodecyl sulfate. Hybridization patterns are visualized using autoradiography or an alternative imaging means and compared.

XI. Microarrays

The linkage or synthesis of array elements upon a microarray can be achieved utilizing photolithography, piezoelectric printing (ink-jet printing; see, e.g., Baldeschweiler et al., supra), mechanical microspotting technologies, and derivatives thereof. The substrate in each of the aforementioned technologies should be uniform and solid with a non-porous surface (Schena, M., ed. (1999) DNA Microarrays: A Practical Approach, Oxford University Press, London). Suggested substrates include silicon, silica, glass slides, glass chips, and silicon wafers. Alternatively, a procedure analogous to a dot or slot blot may also be used to arrange and link elements to the surface of a substrate using thermal, UV, chemical, or mechanical bonding procedures. A typical array may be produced using available methods and machines well known to those of ordinary skill in the art and may contain any appropriate number of elements (Schena, M. et al. (1995) Science 270:467-470; Shalon, D. et al. (1996) Genome Res. 6:639-645; Marshall, A. and J. Hodgson (1998) Nat. Biotechnol. 16:27-31).

Full length cDNAs, Expressed Sequence Tags (ESTs), or fragments or oligomers thereof may comprise the elements of the microarray. Fragments or oligomers suitable for hybridization can be selected using software well known in the art such as LASERGENE software (DNASTAR). The array elements are hybridized with polynucleotides in a biological sample. The polynucleotides in the biological sample are conjugated to a fluorescent label or other molecular tag for ease of detection. After hybridization, nonhybridized nucleotides from the biological sample are removed, and a fluorescence scanner is used to detect hybridization at each array element. Alternatively, laser desorbtion and mass spectrometry may be used for detection of hybridization. The degree of complementarity and the relative abundance of each polynucleotide which hybridizes to an element on the microarray may be assessed. In one embodiment, microarray preparation and usage is described in detail below.

Tissue or Cell Sample Preparation

Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and poly(A)⁺ RNA is purified using the oligo-(dT) cellulose method. Each poly(A)⁺ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oligo-(dT) primer (21 mer), 1× first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Biosciences). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng poly(A)⁺ RNA with GEMBRIGHT kits (Incyte). Specific control poly(A)⁺ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA. After incubation at 37° C. for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C. to the stop the reaction and degrade the RNA. Samples are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto Calif.) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The sample is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2% SDS.

Microarray Preparation

Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 μg. Amplified array elements are then purified using SEPHACRYL-400 (Amersham Biosciences).

Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester Pa.), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110° C. oven.

Array elements are applied to the coated glass substrate using a procedure described in U.S. Pat. No. 5,807,522, incorporated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide.

Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saline (PBS) (Tropix, Inc., Bedford Mass.) for 30 minutes at 60° C. followed by washes in 0.2% SDS and distilled water as before.

Hybridization

Hybridization reactions contain 9 μl of sample mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5×SSC, 0.2% SDS hybridization buffer. The sample mixture is heated to 65° C. for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cm² coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5×SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C. in a first wash buffer (1×SSC, 0.1% SDS), three times for 10 minutes each at 45° C. in a second wash buffer (0.1×SSC), and dried.

Detection

Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara Calif.) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20× microscope objective (Nikon, Inc., Melville N.Y.). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm×1.8 cm arrayused in the present example is scanned with a resolution of 20 micrometers.

In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially. Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.

The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the sample mixture at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000. When two samples from different sources (e.g., representing test and control cells), each labeled with a different fluorophore, re hybridized to a single array for the purpose of identifying genes that are differentially expressed, he calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.

The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood Mass.) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte). Array elements that exhibited at least about a two-fold change in expression, a signal-to-background ratio of at least 2.5, and an element spot size of at least 40% were identified as differentially expressed using the GEMTOOLS program (Incyte Genomics).

Expression

For example, SEQ ID NO:54 was differentially expressed in human peripheral blood mononuclear cells (PBMCs) treated with 10 ng/ml interleukin 4 (IL-4). Human PBMCs can be classified into discrete cellular populations representing the major cellular components of the immune system. PBMCs contain about 52% lymphocytes (12% B lymphocytes, 40% T lymphocytes {25% CD4+ and 15% CD8+}), 20% NK cells, 25% monocytes, and 3% various cells that include dendritic cells and progenitor cells. The proportions, as well as the biology of these cellular components tend to vary slightly between healthy individuals, depending on factors such as age, gender, past medical history, and genetic background.

IL-4 is a pleiotropic cytokine produced by activated T cells, mast cells, and basopbils. It was initially identified as a B cell differentiation factor (BCDF) and a B cell stimulatory factor (BSF1). Subsequent to the molecular cloning and expression of both human and mouse IL-4, numerous other functions have been ascribed to B cells and other hematopoietic and non-hematopoietic cells including endothelial cells, etc. IL-4 exhibits anti-tumor effects both in vivo and in vitro. Recently, IL-4 was identified as an important regulator for the CD4+ subset (Th1-like vs. Th2-like) development. The biological effects of IL-4 are mediated by the binding of IL-4 to specific cell surface receptors. The functional high-affinity receptor for IL-4 consists of a ligand-binding subunit (IL-4 R) and a second subunit (b chain) that can modulate the ligand binding affinity of the receptor complex In certain cell types, the gamma chain of the IL-2 receptor complex is a functional b chain of the IL-4 receptor complex.

In this experiment, PBMCs were collected from the blood of 6 healthy volunteer donors using standard gradient separation. The PBMCs from each donor were placed in culture for 2 hours in the presence or absence of recombinant IL-4. Treated PBMCs and untreated control PBMCs from the different donors were pooled according to their respective treatment. The expression of SEQ ID NO:54 was significantly decreased by at least two-fold in the PBMCs treated with IL-4.

Also, SEQ ID NO:66 showed differential expression in inflammatory responses as determined by microarray analysis. Compared to untreated peripheral blood mononuclear cells (PBMCs) (12% B lymphocytes, 40% T lymphocytes, 20% NK cells, 25% monocytes, and 3% various cells that include dendritic and progenitor cells), the expression of SEQ ID NO:66 was increased by at least 2 fold in PBMCs treated with either interleukin-1 beta (IL-1 β), Interleukin-6 (IL-6), or TNF-α. IL 1 β is a prototypical pro-inflammatory cytokine; IL-6 is a multifunctional protein important in immune responses; and TNF-α is a pleotropic cytokine which mediates inflammatory responses through signal transduction pathways. Therefore, SEQ ID NO:66 is useful as a diagnostic marker for inflammatory responses.

Further, SEQ ID NO:88 showed increased expression in peripheral blood mononuclear cells (PBMCs) treated with 25 microM prednisone versus untreated cells as determined by microarray analysis. PBMCs from the blood of 6 healthy volunteer donors were incubated for 24 hours in the presence of graded doses of prednisone dissolved in ethanol. In addition, matching PBMCs were treated for the same duration with matching doses of ethanol to monitor the possible effects of the vehicle alone. Treated PBMCs were compared to matching untreated PBMCs maintained in culture for the same duration. Further, SEQ ID NO:88 showed increased expression in PBMCs treated with Staphlococcal endotoxin B (SEB) versus untreated cells. PBMCs from 7 healthy volunteer donors were stimulated in vitro with SEB for 72 hours. The SEB-treated PBMCs from each donor were compared to PBMCs from the same donor, kept in culture for 24 hours in the absence of SEB. Therefore, in various embodiments, SEQ ID NO:54, SEQ ID NO:66, and SEQ ID NO:88 can be used for one or more of the following: i) monitoring treatment of immune disorders and related diseases and conditions, ii) diagnostic assays for immune disorders and related diseases and conditions, and iii) developing therapeutics and/or other treatments for immune disorders and related diseases and conditions.

Colon cancer develops through a multi-step process in which pre-malignant colonocytes undergo a relatively defined sequence of events leading to tumor formation Factors that contribute to the process of tumor progression and malignant transformation include genetics, mutations, and selection. The expression of SEQ ID NO:54 was significantly decreased by at least two-fold in various experiments involving colon adenocarcinoma tissue compared to uninvolved tissue from the same donor. Further, SEQ ID NO:90 showed differential expression associated with colon cancer, as determined by microarray analysis. Gene expression profiles from the following matched samples were compared: normal colon and colon tumor tissue from a 56-year-old female diagnosed with poorly differentiated metastatic adenocarcinoma of possible ovarian origin and a clinical history of recurrent cecal mass (Huntsman Cancer Institute, Salt Lake City, Utah); normal and tumor samples from a 58-year-old female diagnosed with mucinous adenocarcinoma (Huntsman Cancer Institute, Salt Lake City, Utah); normal and tumor samples from an 83-year-old female diagnosed with colon cancer (Huntsman Cancer Institute, Salt Lake City, Utah); and normal and tumor samples from a 64-year-old female diagnosed with moderately differentiated colon adenocarcinoma (Huntsman Cancer Institute, Salt Lake City, Utah). The expression of SEQ ID NO:90 was downregulated by at least two-fold in tumor tissues as compared to normal colon tissue. Therefore, in various embodiments, SEQ ID NO:54 and SEQ ID NO:90 can be used for one or more of the following: i) monitoring treatment of colon cancer, ii) diagnostic assays for colon cancer, and iii) developing therapeutics and/or other treatments for colon cancer.

As with most tumors, prostate cancer develops through a multistage progression ultimately resulting in an aggressive tumor phenotype. The initial step in tumor progression involves the hyper-proliferation of normal luminal and/or basal epithelial cells. Androgen responsive cells become hyperplastic and evolve into early-stage tumors. Although early-stage tumors are often androgen sensitive and respond to androgen ablation, a population of androgen independent cells evolve from the hyperplastic population. These cells represent a more advanced form of prostate tumor that may become invasive and potentially become metastatic to the bone, brain, or lung. The expression of SEQ ID NO:55 was differentially expressed in DU145 cells, a line of prostate carcinoma cells isolated from a metastatic site in the brain of a 69-year old male with widespread metastatic prostate carcinoma, as compared to PrEC cells, a primary prostate epithelial cell line isolated from a normal donor. DU145 has no detectable sensitivity to hormones; forms colonies in semi-solid medium; is only weakly positive for acid phosphatase; and cells are negative for prostate specific antigen (PSA). The expression of SEQ ID NO:55 was increased by at least two-fold in prostate tumor cells.

Additional experiments conducted to compare gene expression profiles yielded differential expression of SEQ ID NO:55. PrEC/3 is a primary prostate epithelial cell line isolated from a normal donor. Prostate carcinoma cell lines DU145 and PC3 (metastatic prostate adenocarcinoma) were compared to PrEC/3 cells. Under these conditions, the expression of SEQ ID NO:55 was increased by at least two-fold in the tumor cell lines.

In a similar experiment, the gene expression profiles of prostate carcinoma cell lines DU145 and LNCaP grown under optimal conditions were compared to those of PrEC/3s grown under restrictive conditions. The expression of SEQ ID NO:55 was decreased by at least two-fold in the tumor cell lines.

Also, SEQ ED NO:69 and SEQ ID NO:70 showed differential expression in prostate adenocarcinoma cells versus normal prostate epithelial cells as determined by microarray analysis. The prostate adenocarcinoma cell line was isolated from a metastatic site in the bone of a 62 year old male with grade IV prostate adenocarcinoma. The expression of SEQ ID NO:69 and SEQ ID NO:70 were increased by at least two fold in a prostate carcinoma cell line relative to normal prostate epithelial cells. Therefore, in various embodiments, SEQ ID NO:55 and SEQ ID NO:69-70 can be used for one or more of the following: i) monitoring treatment of prostate cancer, ii) diagnostic assays for prostate cancer, and iii) developing therapeutics and/or other treatments for prostate cancer.

Lung cancers are divided into four histopathologically distinct groups. Three groups (squamous cell carcinoma, adenocarcinoma, and large cell carcinoma) are classified as non-small cell lung cancers (NSCLCs). The fourth group of cancer is referred to as small cell lung cancer (SCLC). Collectively, NSCLCs account for approximately 70% of cases while SCLCs account for approximately 18% of all cases. Pair comparisons were performed in which normal lung tissue and lung tumor tissue from the same donor were examined. Two squamous cell carcinomas were compared to same-donor normal lung tissue, yielding an increase in the expression of SEQ ID NO;55 by at least two-fold in all cases. Further, SEQ ID NO:86 showed differential expression in lung tumor tissue as determined by microarray analysis. Lung cancer is the leading cause of cancer death for men and the second leading cause of cancer death for women in the U.S. Lung cancers are divided into four histopathologically distinct groups. Three groups (squamous cell carcinoma, adenocarcinoma and large cell carcinoma) are classified as non-small cell lung cancers, while the fourth group is classified as small cell lung cancer. Non-small cell lung cancers account for about 70% of lung cancer cases. Pair comparisons of normal and tumor tissue were performed with matched tissue samples from a 73-year old male patient exhibiting squamous cell carcinoma Results showed that expression of SEQ ID NO:86 in the tumor tissue is decreased by at least two-fold. Therefore, in various embodiments, SEQ ID NO:55 and SEQ ID NO:86 can be used for one or more of the following: i) monitoring treatment of lung cancer, ii) diagnostic assays for lung cancer, and iii) developing therapeutics and/or other treatments for lung cancer.

In another example, as determined by microarray analysis, SEQ ID NO:65 showed differential expression when comparing cells from a metastatic breast tumor cell line versus primary breast epithelial cells and non-malignant mammary epithelial cells. The metastatic breast tumor cell line, MDA-mb-23 1, was derived from the pleural effusion of a 51-year-old female with metastatic breast carcinoma; the primary breast epithelial cell line, HMEC was isolated from a normal donor; and the non-malignant mammary epithelial cell line, MCF10A, was isolated from a 36-year-old female with fibrocystic breast disease. All cell cultures were propagated in a defined media, according to the supplier's recommendations and grown to 70-80% confluence prior to RNA isolation. The microarray experiments showed that the expression of SEQ ID NO:65 was increased by at least two fold in the metastatic breast tumor cell line relative to the primary breast epithelial cells and the non-malignant mammary epithelial cells. Therefore, in various embodiments, SEQ ID NO:65 can be used for one or more of the following: i) monitoring treatment of breast cancer, ii) diagnostic assays for breast cancer, and iii) developing therapeutics and/or other treatments for breast cancer.

SEQ ID NO:65 also showed differential expression in preadipocytes versus differentiated adipocytes as determined by microarray analysis. The primary function of adipose tissue is the ability to store and release fat during periods of feeding and fasting. Understanding how the various molecules regulate adiposity in physiological and pathological situations is important for developing diagnostic and therapeutic tools for human obesity. Adipose tissue is also one of the primary target tissues for insulin, and adipogenesis and insulin resistance are linked in non-insulin dependent diabetes mellitus. Cytologically, the conversion of a preadipocytes into mature adipocytes is characterized by deposition of fat droplets around the nuclei. The conversion process in vivo can be induced by thiazolidinediones and other peroxisome proliferator-activated receptor gamma (PPARγ) agonists (Adams et al. (1997) J. Clin. Invest. 100:3149-3153) which are new classes of anti-diabetic agents which improve insulin sensitivity and reduce plasma glucose and blood pressure in patients with type II diabetes. Some PPARγ agents have been proven to induce human adipocyte differentiation. For these assays, human primary preadipocytes were isolated from adipose tissue of a 36 year old healthy female with body mass index 27.7 and a 40 year old healthy female with a body mass index of 32.47. The preadipocytes were cultured and induced to differentiate into adipocytes by culturing them in a medium containing PPARγ agonist and human insulin. The microarray experiments showed that the expression of SEQ ID NO:65 was decreased by at least two fold in preadipocytes treated with PPARγ agonists and insulin relative to untreated preadipocytes. Therefore, SEQ ID NO:65 is useful as a diagnostic marker or as a potential therapeutic target for obesity and diabetes. Therefore, in various embodiments, SEQ ID NO:65 can be used for one or more of the following: i) monitoring treatment of obesity and diabetes, ii) diagnostic assays for obesity and diabetes, and iii) developing therapeutics and/or other treatments for obesity and diabetes.

In another example, SEQ ID NO:71 showed differential expression in human ovarian adenocarcenomic tissue as compared to normal ovarian tissue from the same donor. Ovarian cancer is the leading cause of death from a gynecologic cancer. The majority of ovarian cancers are derived from epithelial cells, and 70% of patients with epithelial ovarian cancers present with late-stage disease. As a result the loingterm survival rates for this disease are very low. Identification of early stage markers for ovarian cancer would significantly increase the survival rate. The molecular events that lead to ovarian cancer are poorly understood. Some of the known aberrations include mutation of p53 and microsatellite instability. Since gene expression patterns likely vary when normal ovary is compared to ovarian tumors we have examined gene expression inm these tissues to identify possible markers for ovarian cancer. The expression of SEQ ID NO:71 was significantly increased by at least two-fold in ovarian tissue as compared to normal tissue. Therefore, in various embodiments, SEQ ID NO:71 can be used for one or more of the following: i) monitoring treatment of ovarian cancer, ii) diagnostic assays for ovarian cancer, and iii) developing therapeutics and/or other treatments for ovarian cancer.

The effects upon liver metabolism and hormone clearance mechanisms are important to understand the pharmacodynamics of a drug. For example, the human C3A cell line is a clonal derivative of HepG2/C3 (hepatoma cell line, isolated from a 15-year-old male with liver tumor), which was selected for strong contact inhibition of growth. The use of a clonal population enhances the reproducibility of the cells. C3A cells have many characteristics of primary human hepatocytes in culture: i) expression of insulin receptor and insulin-like growth factor II receptor; ii) secretion of a high ratio of serum albumin compared with α-fetoprotein; iii) conversion of ammonia to urea and glutamine; iv) metabolism of aromatic amino acids; and v) proliferation in glucose-free and insulin-free medium. The C3A cell line is now well established as an in vitro model of the mature human liver (Mickelson et al (1995) Hepatology 22:866-875; Nagendra et al (1997) Am. J. Physiol 272:G408-G416). In another example, SEQ ID NO:75, SEQ ID NO:77-81 and SEQ ID NO:84 showed increased expression in C3A cells treated with a beclometasone, betamethasone, budesonide, medroxyprogesterone, prednisone, and progesterone, versus untreated C3A cells, as determined by microarray analysis. Therefore, in various embodiments, SEQ ID NO:75, SEQ ID NO:77-81 and SEQ ID NO:84 can be used for one or more of the following: i) monitoring treatment of liver and immune disorders and related diseases and conditions, ii) diagnostic assays for liver and immune disorders and related diseases and conditions, and iii) developing therapeutics and/or other treatments for liver and immune disorders and related diseases and conditions.

XII. Complementary Polynucleotides

Sequences complementary to the INTSIG-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring INTSIG. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and the coding sequence of INTSIG. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the INTSIG-encoding transcript.

XIII. Expression of INTSIG

Expression and purification of INTSIG is achieved using bacterial or virus-based expression systems. For expression of INTSIG in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL2l(DE3). Antibiotic resistant bacteria express INTSIG upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expression of INTSIG in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding INTSIG by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus (Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945).

In most expression systems, INTSIG is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma japoiticum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Biosciences). Following purification, the GST moiety can be proteolytically cleaved from INTSIG at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel et al. (supra, ch 10 and 16). Purified INTSIG obtained by these methods can be used directly in the assays shown in Examples XVII, XVIII, and XVIII, where applicable.

XIV. Functional Assays

INTSIG function is assessed by expressing the sequences encoding INTSIG at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include PCMV SPORT plasmid (Invitrogen, Carlsbad CA) and PCR3.1 plasmid (Invitrogen), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell line, for example, an endothelial or hematopoietic cell line, using either liposome formulations or electroporatiotl 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-transfected. Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64, or a CD64-GFP fusion protein Flow cytometry (FCM), an automated, laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994; Flow Cytometry, Oxford, New York N.Y.).

The influence of INTSIG on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding INTSIG and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success N.Y.). mRNA can be purified from the cells using methods well known by those of skill in the art Expression of mRNA encoding INTSIG and other genes of interest can be analyzed by northern analysis or microarray techniques.

XV. Production of INTSIG Specific Antibodies

INTSIG substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M. G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize animals (e.g., rabbits, mice, etc.) and to produce antibodies using standard protocols.

Alternatively, the INTSIG amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art (Ausubel et al, supra, ch 11).

Typically, oligopeptides of about 15 residues in length are synthesized using an ABI 431A peptide synthesizer (Applied Biosystems) using FMOC chemistry and coupled to KLH (Sigma-Aldrich, St. Louis Mo.) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity (Ausubel et al., supra). Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide and anti-INTSIG activity by, for example, binding the peptide or INTSIG to a substrate, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG.

XVI. Purification of Naturally Occurring INTSIG Using Specific Antibodies

Naturally occurring or recombinant INTSIG is substantially purified by immunoaffinity chromatography using antibodies specific for INTSIG. An immunoaffinity column is constructed by covalently coupling anti-INTSIG antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Biosciences). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

Media containing INTSIG are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of INTSIG (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/INTSIG binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and INTSIG is collected.

XVII. Identification of Molecules Which Interact with INTSIG

INTSIG, or biologically active fragments thereof, are labeled with ¹²⁵I Bolton-Hunter reagent (Bolton, A. E. and W. M. Hunter (1973) Biochem. J. 133:529-539). Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled INTSIG, washed, and any wells with labeled INTSIG complex are assayed. Data obtained using different concentrations of INTSIG are used to calculate values for the number, affinity, and association of INTSIG with the candidate molecules.

Alternatively, molecules interacting with INTSIG are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989; Nature 340:245-246), or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (Clontech).

INTSIG may also be used in the PATHCALLING process (CuraGen Corp., New Haven Conn.) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K et al. (2000) U.S. Pat. No. 6,057,101).

XVIII. Demonstration of INTSIG Activity

INTSIG activity is associated with its ability to form protein-protein complexes and is measured by its ability to regulate growth characteristics of NIH3T3 mouse fibroblast cells. A cDNA encoding INTSIG is subcloned into an appropriate eukaryotic expression vector. This vector is transfected into NIH3T3 cells using methods known in the art Transfected cells are compared with non-transfected cells for the following quantifiable properties: growth in culture to high density, reduced attachment of cells to the substrate, altered cell morphology, and ability to induce tumors when injected into immunodeficient mice. The activity of INTSIG is proportional to the extent of increased growth or frequency of altered cell morphology in NIH3T3 cells transfected with INTSIG.

Alternatively, INTSIG activity is measured by binding of INTSIG to radiolabeled formin polypeptides containing the proline-rich region that specifically binds to SH3 containing proteins (Chan, D. C. et al. (1996) EMBO J. 15:1045-1054). Samples of INTSIG are run on SDS-PAGE gels, and transferred onto nitrocellulose by electroblotting. The blots are blocked for 1 hr at room temperature in TBST (137 mM NaCl, 2.7 mM KCl, 25 mM Tris (pH 8.0) and 0.1% Tween-20) containing non-fat dry milk. Blots are then incubated with TBST containing the radioactive formin polypeptide for 4 hrs to overnight After washing the blots four times with TBST, the blots are exposed to autoradiographic film. Radioactivity is quantitated by cutting out the radioactive spots and counting them in a radioisotope counter. The amount of radioactivity recovered is proportional to the activity of INTSIG in the assay.

Alternatively, PDE activity of INTSIG is measured by monitoring the conversion of a cyclic nucleotide (either cAMP or cGMP) to its nucleotide monophosphate. The use of tritium-containing substrates such as ³H-cAMP and ³H-cGMP, and 5′ nucleotidase from snake venom, allows the PDE reaction to be followed using a scintillation counter. cAMP-specific PDE activity of INTSIG is assayed by measuring the conversion of ³H-cAMP to ³H-adenosine in the presence of INTSIG and 5′ nucleotidase. A one-step assay is ran using a 100 μl reaction containing 50 mM Tris-HCl, pH 7.5, 10 mM MgCl₂, 0.1 unit 5′ nucleotidase (from Crotalus atrox venom), 0.0062-0.1 μM ³H-cAMP, and various concentrations of cAMP (0.0062-3 mM). The reaction is started by the addition of 25 μl of diluted enzyme supernatant. Reactions are run directly in mini Poly-Q scintillation vials (Beckman Instruments, Fullerton Calif.). Assays are incubated at 37° C. for a time period that would give less than 15% cAMP hydrolysis to avoid non-linearity associated with product inbibition. The reaction is stopped by the addition of 1 ml of Dowex (Dow Chemical, Midland Mich.) AG1×8 (Cl form) resin (1:3 slurry). Three ml of scintillation fluid are added, and the vials are mixed. The resin in the vials is allowed to settle for one hour before counting. Soluble radioactivity associated with ³H-adenosine is quantitated using a beta scintillation counter. The amount of radioactivity recovered is proportional to the cAMP-specific PDE activity of INTSIG in the reaction. For inhibitor or agonist studies, reactions are carried out under the conditions described above, with the addition of 1% DMSO, 50 nM cAMP, and various concentrations of the inhibitor or agonist Control reactions are carried out with all reagents except for the enzyme aliquot.

In an alternative assay, cGMP-specific PDE activity of INTSIG is assayed by measuring the conversion of ³H-cGMP to ³H-guanosine in the presence of INTSIG and 5′ nucleotidase. A one-step assay is run using a 100 μl reaction containing 50 mM Tris-HCl pH 7.5, 10 mM MgCl₂, 0.1 unit 5′ nucleotidase (from Crotalus atrox venom), and 0.0064-2.0 μM ³H-cGMP. The reaction is started by the addition of 25 μl of diluted enzyme supernatant Reactions are run directly in mini Poly-Q scintillation vials (Beckman Instruments). Assays are incubated at 37° C. for a time period that would yield less than 15% cGMP hydrolysis in order to avoid non-linearity associated with product inhibition. The reaction is stopped by the addition of 1 ml of Dowex (Dow Chemical, Midland Mich.) AG1×8 (Cl form) resin (1:3 slurry). Three ml of scintillation fluid are added, and the vials are mixed. The resin in the vials is allowed to settle for one hour before counting. Soluble radioactivity associated with ³H-guanosine is quantitated using a beta scintillation counter. The amount of radioactivity recovered is proportional to the cGMP-specific PDE activity of INTSIG in the reaction. For inhibitor or agonist studies, reactions are carried out under the conditions described above, with the addition of 1% DMSO, 50 nM cGMP, and various concentrations of the inhibitor or agonist Control reactions are carried out with all reagents except for the enzyme aliquot.

Alternatively, INTSIG protein kinase activity is measured by quantifying the phosphorylation of an appropriate substrate in the presence of gamma-labeled ³²P-ATP. INTSIG is incubated with the substrate, ³²P-ATP, and an appropriate kinase buffer. The ³²P incorporated into the product is separated from free ³²P-ATP by electrophoresis, and the incorporated ³²P is quantified using a beta radioisotope counter. The amount of incorporated ³P is proportional to the protein kinase activity of INTSIG in the assay. A determination of the specific amino acid residue phosphorylated by protein kinase activity is made by phosphoamino acid analysis of the hydrolyzed protein.

Alternatively, an assay for INTSIG protein phosphatase activity measures the hydrolysis of para-nitrophenyl phosphate (PNPP). INTSIG is incubated together with PNPP in HEPES buffer pH 7.5, in the presence of 0.1% β-mercaptoethanol at 37° C. for 60 min. The reaction is stopped by the addition of 6 ml of 10 N NaOH, and the increase in light absorbance of the reaction mixture at 410 nm resulting from the hydrolysis of PNPP is measured using a spectrophotometer. The increase in light absorbance is proportional to the activity of INTSIG in the assay (Diamond, R. H. et al. (1994) Mol. Cell Biol. 14:3752-3762).

Alternatively, adenylyl cyclase activity of INTSIG is demonstrated by the ability to convert ATP to cAMP (Mittal, C. K. (1986) Meth. Enzymol. 132:422-428). In this assay INTSIG is incubated with the substrate [α-³²P]ATP, following which the excess substrate is separated from the product cyclic [³²P] AMP. INTSIG activity is determined in 12×75 mm disposable culture tubes containing 5 μl of 0.6 M Tris-HCl, pH 7.5, 5 μl of 0.2 M MgCl₂, 5 μl of 150 mM creatine phosphate containing 3 units of creatine phosphokinase, 5 μl of 4.0 mM 1-methyl-3-isobutylxanthine, 5 μl of 20 mM cAMP, 5 μl 20 mM dithiothreitol, 5 μl of 10 mM ATP, 10 μl [α³²P]ATP (2-4×106 cpm), and water in a total volume of 100 μl. The reaction mixture is prewarmed to 30° C. The reaction is initiated by adding INTSIG to the prewarmed reaction mixture. After 10-15 minutes of incubation at 30° C., the reaction is terminated by adding 25 μl of 30% ice-cold trichloroacetic acid (TCA). Zero-time incubations and reactions incubated in the absence of INTSIG are used as negative controls. Products are separated by ion exchange chromatography, and cyclic [³²P] AMP is quantified using a β-radioisotope counter. The INTSIG activity is proportional to the amount of cyclic [³²P] AMP formed in the reaction.

An alternative assay measures INTSIG-mediated G-protein signaling activity by monitoring the mobilization of Ca²⁺ as an indicator of the signal transduction pathway stimulation. (See, e.g., Grynkiewicz, G. et al (1985) J. Biol. Chem. 260:3440; McColl, S. et al. (1993) J. Immunol. 150:4550-4555; and Aussel supra). The assay requires preloading neutropbils or T cells with a fluorescent dye such as FURA-2 or BCECF (Universal Imaging Corp, Westchester Pa.) whose emission characteristics are altered by Ca²⁺ binding. When the cells are exposed to one or more activating stimuli artificially (e.g., anti-CD3 antibody ligation of the T cell receptor) or physiologically (e.g., by allogeneic stimulation), Ca²⁺ flux takes place. This flux can be observed and quantified by assaying the cells in a fluorometer or fluorescent activated cell sorter. Measurements of Ca²⁺ flux are compared between cells in their normal state and those transfected with INTSIG. Increased Ca²⁺ mobilization attributable to increased INTSIG concentration is proportional to INTSIG activity.

Alternatively, GTP-binding activity of INTSIG is determined in an assay that measures the binding of INTSIG to [α-³²P]-labeled GTP. Purified INTSIG is first blotted onto filters and rinsed in a suitable buffer. The filters are then incubated in buffer containing radiolabeled [α-³²P]-GTP. The filters are washed in buffer to remove unbound GTP and counted in a radioisotope counter. Non-specific binding is determined in an assay that contains a 100-fold excess of unlabeled GTP. The amount of specific binding is proportional to the activity of INTSIG.

Alternatively, GTPase activity of INTSIG is determined in an assay that measures the conversion of [α-³²P]-GTP to [α-³²P]-GTP. INTSIG is incubated with [α-³²P]-GTP in buffer for an appropriate period of time, and the reaction is terminated by heating or acid precipitation followed by centrifugation. An aliquot of the supernatant is subjected to polyacrylamide gel electrophoresis (PAGE) to separate GDP and GTP together with unlabeled standards. The GDP spot is cut out and counted in a radioisotope counter. The amount of radioactivity recovered in GDP is proportional to the GTPase activity of INTSIG.

Alternatively, INTSIG activity is measured by quantifying the amount of a non-hydrolyzable GTP analogue, GTPγS, bound over a 10 minute incubation period. Varying amounts of INTSIG are incubated at 30° C. in 50 mM Tris buffer, pH 7.5, containing 1 mM dithiothreitol, 1 mM EDTA and 1 μM [³⁵S]GTPγS. Samples are passed through nitrocellulose filters and washed twice with a buffer consisting of 50 mM Tris-HCl, pH 7.8, 1 mM NaN₃, 10 mM MgCl₂, 1 mM EDTA, 0.5 mM dithiothreitol, 0.01 mM PMSF, and 200 mM NaCl. The filter-bound counts are measured by liquid scintillation to quantify the amount of bound [³⁵S]GTPγS. INTSIG activity may also be measured as the amount of GTP hydrolysed over a 10 minute incubation period at 37° C. INTSIG is incubated in 50 mM Tris-HCl buffer, pH 7.8, containing 1 mM dithiothreitol, 2 mM EDTA, 10 μM [α-³²P]GTP, and 1 μM H-rab protein. GTPase activity is initiated by adding MgCl₂ to a final concentration of 10 mM. Samples are removed at various time points, mixed with an equal volume of ice-cold 0.5 mM EDTA, and frozen. Aliquots are spotted onto polyethyleneimine-cellulose thin layer chromatography plates, which are developed in 1M LiCl, dried, and autoradiographed. The signal detected is proportional to INTSIG activity.

Alternatively, INTSIG activity may be demonstrated as the ability to interact with its associated LMW GTPase in an in vitro binding assay. The candidate LMW GTPases are expressed as fusion proteins with glutathione S-transferase (GST), and purified by affinity chromatography on glutathione-Sepharose. The LMW GTPases are loaded with GDP by incubating 20 mM Tris buffer, pH 8.0, containing 100 mM NaCl, 2 mM EDTA, 5 mM MgCl₂, 0.2 mM DTT, 100 μM AMP-PNP and 10 μM GDP at 30° C. for 20 minutes. INTSIG is expressed as a FLAG fusion protein in a baculovirus system. Extracts of these baculovirus cells containing INTSIG-FLAG fusion proteins are precleared with GST beads, then incubated with GST-GTPase fusion proteins. The complexes formed are precipitated by glutathione-Sepharose and separated by SDS-polyacrylamide gel electrophoresis. The separated proteins are blotted onto nitrocellulose membranes and probed with commercially available anti-FLAG antibodies. INTSIG activity is proportional to the amount of INTSIG-LAG fusion protein detected in the complex.

The role of INTSIG can be assayed in vitro by monitoring the mobilization of Ca⁺⁺ as part of the signal transduction pathway. (See, e.g., Grynkievicz, G. et al. (1985) J. Biol. Chem. 260:3440; McColl, S. et al. (1993) J. Immunol. 150:4550-4555; and Aussel, C. et al. (1988) J. Immunol. 140:215-220.) The assay requires preloading neutrophils or T cells with a fluorescent dye such as FURA-2. Upon binding Ca⁺⁺, FURA-2 exhibits an absorption shift that can be observed by scanning the excitation spectrum between 300 and 400 nm, while monitoring the emission at 510 nm. When the cells are exposed to one or more activating stimuli artificially (i.e., anti-CD3 antibody ligation of the T cell receptor) or physiologically (i.e., by allogeneic stimulation), Ca⁺⁺ flux takes place. Ca⁺⁺ flux results from the release of Ca⁺⁺ from intracellular organelles or from Ca⁺⁺ entry into the cell through activated Ca⁺⁺ channels. This flux can be observed and quantified by assaying the cells in a fluorometer or fluorescence activated cell sorter. Measurements of Ca⁺⁺ flux are compared between cells in their normal state and those preloaded with INTSIG. Increased mobilization attributable to increased INTSIG availability results in increased emission.

Another alternative assay to detect INTSIG activity is the use of a yeast two-hybrid system (Zalcman, G. et al. (1996) J. Biol. Chem. 271:30366-30374). Specifically, a plasmid such as pGAD1318 which may contain the coding region of INTSIG can be used to transform reporter L40 yeast cells which contain the reporter genes LacZ and HIS3 downstream from the binding sequences for LexA. These yeast cells have been previously transformed with a pLexA-Rab6-GDP (mouse) plasmid or with a plasmid which contains pLexA-lamin C. The pLEXA-lamin C cells serve as a negative control. The transformed cells are plated on a histidine-free medium and incubated at 30° C. for 3 days. His⁺ colonies are subsequently patched on selective plates and assayed for β-galactosidase activity by a filter assay. INTSIG binding with Rab6-GDP is indicated by positive His⁺/lacZ⁺ activity for the cells transformed with the plasmid containing the mouse Rab6-GDP and negative His⁺/lacZ⁺ activity for those transformed with the plasmid containing lamin C.

Alternatively, INTSIG activity is measured by binding of INTSIG to a substrate which recognizes WD-40 repeats, such as ElonginB, by coimmunoprecipitation (Kamura, T. et al. (1998) Genes Dev. 12:3872-3881). Briefly, epitope tagged substrate and INTSIG are mixed and immunoprecipitated with commercial antibody against the substrate tag. The reaction solution is run on SDS-PAGE and the presence of INTSIG visualized using an antibody to the INTSIG tag. Substrate binding is proportional to INTSIG activity.

Alternatively, INTSIG activity is measured by its inclusion in coated vesicles. INTSIG can be expressed by transforming a mammalian cell line such as COS7, HeLa, or CHO with a eukaryotic expression vector encoding INTSIG. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. A small amount of a second plasmid, which expresses any one of a number of marker genes, such as β-galactosidase, is co-transformed into the cells in order to allow rapid identification of those cells which have taken up and expressed the foreign DNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of INTSIG and β-galactosidase.

In the alternative, INTSIG activity is measured by its ability to alter vesicle trafficking pathways. Vesicle trafficking in cells transformed with INTSIG is examined using fluorescence microscopy. Antibodies specific for vesicle coat proteins or typical vesicle trafficking substrates such as transferrin or the mannose-6-phosphate receptor are commercially available. Various cellular components such as ER, Golgi bodies, peroxisomes, endosomes, lysosomes, and the plasmalemma are examined. Alterations in the numbers and locations of vesicles in cells transformed with INTSIG as compared to control cells are characteristic of INTSIG activity. Transformed cells are collected and cell lysates are assayed for vesicle formation. A non-hydrolyzable form of GTP, GTPγS, and an ATP regenerating system are added to the lysate and the mixture is incubated at 37° C. for 10 minutes. Under these conditions, over 90% of the vesicles remain coated (Orci, L. et al. (1989) Cell 56:357-368). Transport vesicles are salt-released from the Golgi membranes, loaded under a sucrose gradient, centrifuged, and fractions are collected and analyzed by SDS-PAGE. Co-localization of INTSIG with clathrin or COP coatamer is indicative of INTSIG activity in vesicle formation. The contribution of INTSIG in vesicle formation can be confirmed by incubating lysates with antibodies specific for INTSIG prior to GTPγS addition. The antibody will bind to INTSIG and interfere with its activity, thus preventing vesicle formation.

Alternatively, INTSIG activity is measured by the transfer of electrons from (and consequent oxidation of ) NADH to cytochrome b5 when INTSIG is incubated together with NADH and cytochrome b5. The reaction is carried out in an optical cuvette containing aliquots of INTSIG together with 150 mM each of NADH and cytochroine b5 in 1 M Tris-acetate buffer, pH 8.1. The reaction is incubated at 21° C. and the oxidation of NADH is followed by the change in absorption at 340 nm using an ultraviolet spectrophotometer. The activity of INTSIG is proportional to the rate of change of absorption at 340 nm.

Alternatively, INTSIG activity is measured by the transfer of electrons from cytochrome c to an electron acceptor (KCN) in the presence of a reconstituted cytochrome c oxidase enzyme complex containing INTSIG in place of COX4. The reconstituted cytochrome c oxidase is incubated together with cytochrome c and KCN in a suitable buffer. The reaction is carried out in an optical cuvette and monitored by the change in absorption due to oxidation of cytochrome c using a spectrophotometer. Cytochrome c oxidase reconstituted in the absence of INTSIG is used as a negative control. The activity of INTSIG is proportional to the change in optical absorption measured.

In another alternative, INTSIG activity is measured in the reconstituted NADH-D complex by the catalysis of electron transfer from NADH to decylubiquinone (DB). The reaction contains 10 mg/mL NADH-D protein, 20 mM NADH in 50 mM tris-HCL buffer, pH 7.5,50 mM NaCl, and 1 mM KCN. The reaction is started by addition of DB at 2 uM and followed by the change in absorbance at 340 nm due to the oxidation of NADH using an ultraviolet spectrophotometer. NADH-D complex reconstituted in the absence of NHETP-3 is compared as a negative control. The activity of MITO in the reconstituted NADH-D complex is proportional to the rate of change of absorbance at 340 nm.

Various modifications and variations of the described compositions, methods, and systems of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. It will be appreciated that the invention provides novel and useful proteins, and their encoding polynucleotides, which can be used in the drug discovery process, as well as methods for using these compositions for the detection, diagnosis, and treatment of diseases and conditions. Although the invention has been described in connection with certain embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Nor should the description of such embodiments be considered exhaustive or limit the invention to the precise forms disclosed. Furthermore, elements from one embodiment can be readily recombined with elements from one or more other embodiments. Such combinations can form a number of embodiments within the scope of the invention. It is intended that the scope of the invention be defined by the following claims and their equivalents. TABLE 1 Polypeptide Polynucleotide Incyte Incyte Full Incyte SEQ ID Incyte SEQ ID Polynucleotide Length Project ID NO: Polypeptide ID NO: ID Clones 2562907 1 2562907CD1 46 2562907CB1 3744219 2 3744219CD1 47 3744219CB1 5515030 3 5515030CD1 48 5515030CB1 90159523CA2 1681532 4 1681532CD1 49 1681532CB1 70845770  5 70845770CD1  50 70845770CB1  90161086CA2, 90161162CA2, 90161178CA2, 90161194CA2 3448184 6 3448184CD1 51 3448184CB1 6322968 7 6322968CD1 52 6322968CB1 6819485 8 6819485CD1 53 6819485CB1 7499882 9 7499882CD1 54 7499882CB1  2699414CA2 6623259 10 6623259CD1 55 6623259CB1 2239208 11 2239208CD1 56 2239208CB1 3821431 12 3821431CD1 57 3821431CB1 6973721 13 6973721CD1 58 6973721CB1 90190080CA2 7499694 14 7499694CD1 59 7499694CB1 2454570 15 2454570CD1 60 2454570CB1 6595652 16 6595652CD1 61 6595652CB1 5770223 17 5770223CD1 62 5770223CB1 7729840 18 7729840CD1 63 7729840CB1 4635167 19 4635167CD1 64 4635167CB1  4637779CA2, 90149670CA2, 90149686CA2, 90149762CA2 7499571 20 7499571CD1 65 7499571CB1 8047234 21 8047234CD1 66 8047234CB1 8217739 22 8217739CD1 67 8217739CB1  413973 23  413973CD1 68  413973CB1 90132956CA2, 90132972CA2, 90132980CA2, 90132996CA2 7501022 24 7501022CD1 69 7501022CB1  182852 25  182852CD1 70  182852CB1 1644979 26 1644979CD1 71 1644979CB1 55111748  27 55111748CD1  72 55111748CB1  3358362 28 3358362CD1 73 3358362CB1 8113230 29 8113230CD1 74 8113230CB1 1785616 30 1785616CD1 75 1785616CB1 71113255  31 71113255CD1  76 71113255CB1  7502098 32 7502098CD1 77 7502098CB1 7502099 33 7502099CD1 78 7502099CB1 7502100 34 7502100CD1 79 7502100CB1 7502750 35 7502750CD1 80 7502750CB1 7502891 36 7502891CD1 81 7502891CB1 2571532 37 2571532CD1 82 2571532CB1 6436087 38 6436087CD1 83 6436087CB1 90150918CA2, 90151002CA2, 90151018CA2, 90151034CA2 7502109 39 7502109CD1 84 7502109CB1 7500262 40 7500262CD1 85 7500262CB1  2099384CA2, 90146970CA2, 90146978CA2, 90146986CA2, 90146994CA2, 90147070CA2, 90147078CA2, 90147086CA2, 90147094CA2, 2172094 41 2172094CD1 86 2172094CB1 7413862 42 7413862CD1 87 7413862CB1 90162214CA2, 90162222CA2, 90162306CA2, 90162346CA2, 7503755 43 7503755CD1 88 7503755CB1 7500488 44 7500488CD1 89 7500488CB1 90009370CA2 7510676 45 7510676CD1 90 7510676CB1

TABLE 2 Polypeptide GenBank ID NO: SEQ Incyte or PROTEOME Probability ID NO: Polypeptide ID ID NO: Score Annotation 1 2562907CD1 g484102 1.30E−129 [Homo sapiens] guanine nucleotide regulatory protein Chan, A. M. L. et al. (1994) Expression cDNA cloning of a novel oncogene with sequence similarity to regulators of small GTP-binding proteins. Oncogene 9: 1057 1063 2 3744219CD1 g1814396 8.60E−250 [Mus musculus] rap1/rap2 interacting protein 3 5515030CD1 g607003 8.90E−66 [Podospora anserina] beta transducin-like protein Saupe, S. et al. (1995) A gene responsible for vegetative incompatibility in the fungus Podospora anserina encodes a protein with a GTP-binding motif and G beta homologous domain. Gene 162: 135-139 4 1681532CD1 g10504266 7.40E−09 [Mus musculus] betaPix-c Kim, S. et al. (2000) Molecular cloning of neuronally expressed mouse betaPix isoforms. Biochem. Biophys. Res. Commun. 272: 721-725 5 70845770CD1  g6665778 5.40E−106 [Mus musculus] cyclin ania-6b 6 3448184CD1 g3015538 0.0 [Homo sapiens] nuclear dual-specificity phosphatase Cui, X. et al. (1998) Nature Genet. 18 (4), 331-337 7 6322968CD1 g1339910 1.50E−57 [Homo sapiens] DOCK180 protein Hasegawa, H. et al. (1996) Mol. Cell. Biol. 16 (4), 1770-1776 8 6819485CD1 g6651021 3.30E−195 [Mus musculus] semaphorin cytoplasmic domain-associated protein 3B 9 7499882CD1 g18655335 0.0 [Homo sapiens] epidermal growth factor receptor pathway substrate 8 related protein 3 10 6623259CD1 g4580011 1.00E−138 [Homo sapiens] TRAF4 associated factor 1 11 2239208CD1 g7380947 0.0 [Homo sapiens] Gem-interacting protein 12 3821431CD1 g3687394 1.20E−62 [Homo sapiens] ranbp3-a Mueller, L. et al. (1998) FEBS Lett. 427 (3), 330-336 13 6973721CD1 g11496167 4.80E−07 [Mus musculus] RPGR-interacting protein Hong, D. H. et al. (2001) J. Biol. Chem. 276 (15), 12091-12099 14 7499694CD1 g3687394 3.50E−56 [Homo sapiens] ranbp3-a Mueller, L. et al. (1998 FEBS Lett. 427 (3), 330-336 15 2454570CD1 g20977056 0.0 [Homo sapiens] RGS3 isoform PDZ-RGS3 Kehrl, J. H. et al. (2002) Additional 5′ Exons in the RGS3 Locus Generate Multiple mRNA Transcripts, One of Which Accounts for the Origin of Human PDZ-RGS3. Genomics 79 (6), 860-868 16 6595652CD1 g3687387 2.50E−293 [Homo sapiens] ranbp3 Mueller, L. et al. (1998) FEBS Lett. 427 (3), 330-336 17 5770223CD1 g4101720 3.20E−131 [Mus musculus] lymphocyte specific formin related protein 18 7729840CD1 g3059135 7.20E−200 [Homo sapiens] oligophrenin 1 Bienvenu, T. et al. (1997) Mapping of the X-breakpoint involved in a balanced X; 12 translocation in a female with mild mental retardation. Eur. J. Hum. Genet. 5: 105-109 Billuart, P. et al. (1998) Oligophrenin-1 encodes a rhoGAP protein involved in X- linked mental retardation. Nature 392: 923-926 19 4635167CD1 g10504968 2.70E−19 [Drosophila melanogaster] rho guanine nucleotide exchange factor 4 20 7499571CD1 g3834629 0.0 [Mus musculus] diaphanous-related formin; p134 mDia2 Alberts, A. S. et al. (1998) Analysis of RhoA-binding proteins reveals an interaction domain conserved in heterotrimeric G protein beta subunits and the yeast response regulator protein Skn7. J. Biol. Chem. 273: 8616-8622 21 8047234CD1 g5809678 0.0 [Homo sapiens] sperm membrane protein BS-63 Wang, L. F. et al. (1999) Molecular cloning and characterization of a novel testis- specific nucleoporin-related gene. Arch. Androl. 42: 71-84 22 8217739CD1 g7110160 2.40E−30 [Homo sapiens] guanine nucleotide exchange factor Kourlas, P. J. et al. (2000) Identification of a gene at 11q23 encoding a guanine nucleotide exchange factor: evidence for its fusion with MLL in acute myeloid leukemia. Proc. Natl. Acad. Sci. U.S.A. 97: 2145-2150 23  413973CD1 g3252977 3.60E−12 [Caenorhabditis elegans] Ras-binding protein SUR-8 Sieburth, D. S. et al. (1998) SUR-8, a conserved Ras-binding protein with leucine- rich repeats, positively regulates Ras-mediated signaling in C. elegans. Cell 94: 119-130 24 7501022CD1 g1657837 0.0 [Mus musculus] p116Rip Gebbink, M. F. et al. (1997) Identification of a novel, putative Rho-specific GDP/GTP exchange factor and a RhoA-binding protein: control of neuronal morphology. J Cell Biol. 137: 1603-1613 25  182852CD1 g1657837 0.0 [Mus musculus] p116Rip Gebbink, M. F. et al. (1997) Identification of a novel, putative Rho-specific GDP/GTP exchange factor and a RhoA-binding protein: control of neuronal morphology. J Cell Biol. 137: 1603-1613 26 1644979CD1 g2114473 9.50E−66 [Mus musculus] p140mDia 27 55111748CD1  g13650131 0.0 [Homo sapiens] sorbin and SH3 domain containing 1 Lin WH, et al. (2001) Cloning, mapping, and characterization of the human sorbin and SH3 domain containing 1 (SORBS1) gene: a protein associated with c-Ab1 during insulin signaling in the hepatoma cell line Hep3B. Genomics 74: 12-20 28 3358362CD1 g1694954 9.30E−113 [Homo sapiens] Neuroblastoma g16589064 0.0 [Homo sapiens] putative SH3 domain-containing guanine exchange factor SGEF 29 8113230CD1 g14028714 0.0 [Mus musculus] Rho GTPase-activating protein 30 1785616CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. (1998) Neuron 20: 895-904 A synaptic Ras-GTPase activating protein (p135 SynGAP) inhibited by CaM kinase II Kim, J. H. et al. (1998) Neuron 20: 683-691 SynGAP: a synaptic RasGAP that associates with the PSD-95/SAP90 protein family 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  1.4E−237 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 275381|gap-2-4  2.3E−106 [Caenorhabditis elegans][GTPase activating protein; Activator] Putative GTPase activating protein, putative ortholog of human ras GTPase activating protein-like NGAP 430642|Rasa  3.3E−30 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  7.1E−30 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 31 71113255CD1  g5020264  1.4E−96 [Mus musculus] Cdc42 GTPase-activating protein Lamarche-Vane, N. and Hall, A. (1998) CdGAP, a novel proline-rich GTPase- activating protein for Cdc42 and Rac. J. Biol. Chem. 273: 29172-29177 611278|Cdgap  1.3E−97 [Mus musculus][GTPase activating protein; Activator] Serine-and proline-rich GTPase-activating protein, probably functions inCdc42 and Rac signaling to bring about actin reorganization 309525|  9.3E−67 [Homo sapiens][GTPase activating protein] Protein containing a RhoGAP Hs.169550 domain, has a region of low similarity to murine Mm. 4462, which has GTPase activating activity for the Rac subfamily of ras-related GTP binding proteins, binds SH3 domains, and inhibits Rac-mediated membrane ruffling 331736|Rn.11166   4E−26 [Rattus norvegicus][GTPase activating protein; Activator]N-chimaerin (n- chimerin), ortholog of human CHN1, n-chimerin, which is a GTPase activating protein for rac (a member of the ras family of GTP binding proteins), expressed in neurons and developmentally regulated, has a phorbol ester binding domain 334650|CHN1  5.2E−25 [Homo sapiens][GTPase activating protein; Activator] Alpha 1 chimerin (chimaerin), a GTPase activating protein for rac (a member of the ras family of GTP binding proteins), has divergent SH2 domain at N-terminus but shares C- terminal GTPase activating domain of alpha 1 chimerin 32 7502098CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. supra; Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  6.5E−257 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 275381|gap-2-4  1.9E−108 [Caenorhabditis elegans][GTPase activating protein; Activator] Putative GTPase activating protein, putative ortholog of human ras GTPase activating protein-like NGAP 430642|Rasa  4.8E−30 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  1.0E−29 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 33 7502099CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. supra; Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  5.3E−261 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 275381|gap-2-4  2.0E−116 [Caenorhabditis elegans][GTPase activating protein; Activator] Putative GTPase activating protein, putative ortholog of human ras GTPase activating protein-like NGAP 430642|Rasa  9.9E−34 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  6.4E−33 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 34 7502100CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. supra; Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  1.6E−260 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 430642|Rasa  1.0E−33 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  6.6E−33 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 35 7502750CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. supra; Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  5.5E−234 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 275381|gap-2-4   3E−106 [Caenorhabditis elegans][GTPase activating protein; Activator] Putative GTPase activating protein, putative ortholog of human ras GTPase activating protein-like NGAP 430642|Rasa  3.4E−30 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  7.4E−30 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 36 7502891CD1 g2935448 0.0 [Rattus norvegicus] synaptic ras GTPase-activating protein p135 SynGAP Chen, H. J. et al. supra; Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  1.0E−250 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 430642|Rasa  7.6E−34 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  4.9E−33 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 37 2571532CD1 g7110587  2.4E−185 [Mus musculus] GRP1-associated scaffold protein GRASP Nevrivy, D. J. et al. (2000) Interaction of GRASP, a protein encoded by a novel retinoic acid-induced gene, with members of the cytohesin family of guanine nucleotide exchange factors. J. Biol. Chem. 275: 16827-16836 608424|Grasp  2.2E−186 [Mus musculus][Anchor Protein][Plasma membrane] GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein 340690|PSCDBP  8.6E−48 [Homo sapiens] Protein that contains a leucine zipper and nuclear targeting sequence 38 6436087CD1 g14245732  1.0E−62 [Homo sapiens] rho-GTPase activating protein Furukawa, Y. et al. (2001) Isolation of a novel human gene, ARHGAP9, encoding a rho-GTPase activating protein. Biochem. Biophys. Res. Commun. 284: 643-649 598808|  1.9E−43 [Homo sapiens][GTPase activating protein; Activator]Protein containing a FLJ10971 RhoGAP domain, has moderate similarity to a region of chimaerins (chimerins), which are GTPase activating proteins for rac (a member of the ras family of GTP binding proteins) 331736|Rn.11166  4.1E−34 [Rattus norvegicus][GTPase activating protein; Activator]N-chimaerin (n- chimerin), ortholog of human CHN1, n-chimerin, which is a GTPase activating protein for rac (a member of the ras family of GTP binding proteins), expressed in neurons and developmentally regulated, has a phorbol ester binding domain 334650|CHN1  2.9E−33 [Homo sapiens][GTPase activating protein; Activator] Alpha 1chimerin (chimaerin) a GTPase activating protein for rac (a member of the ras family of GTP binding proteins), has divergent SH2 domain at N-terminus but shares C- terminal GTPase activating domain of alpha 1 chimerin 623606|BCR  2.5E−32 [Homo sapiens][Protein kinase; Transferase; GTPase activating protein; Activator] GTPase-activating protein for p21rac with serine/threonine kinase activity; translocation of the corresponding gene is associated with Philadelphia chromosome-positive chronic myeloid leukemia 39 7502109CD1 g3722229 0.0 [Rattus norvegicus] SynGAP-b Kim, J. H. et al. supra 329630|Rn.9908 0.0 [Rattus norvegicus][GTPase activating protein; Activator]GTPase activating protein (GAP) for Ras, expressed mainly in hippocampal neurons, forms complexes with the synaptic protein PSD-95 and the N-methyl-D-aspartate-type glutamate receptor, activity is inhibited by phosphorylation by CaM kinase II 340956|NGAP  6.9E−256 [Homo sapiens][GTPase activating protein; Activator] GTPase activating protein (GAP) that acts on ras-like proteins 275381|gap-2-4  2.2E−108 [Caenorhabditis elegans][GTPase activating protein; Activator] Putative GTPase activating protein, putative ortholog of human ras GTPase activating protein-like NGAP 430642|Rasa  5.0E−30 [Rattus norvegicus][GTPase activating protein; Activator] RASp21 activator protein, has very strong similarity to human RASA1, which has two isoforms; mutation of the corresponding human gene is associated with tumor formation 661214|RASA1  1.1E−29 [Homo sapiens][GTPase activating protein; Activator; Small molecule-binding protein] GTPase activating protein for the ras GTP binding protein, has two isoforms; mutation of the corresponding gene is associated with tumor formation 40 7500262CD1 g13477291  4.3E−101 [Homo sapiens] ECSIT 430258|Sitpec  5.0E−86 [Mus musculus][Activator] Adaptor protein that is aregulator of MEKK-1, has a role in the activation of NF-kappaB andin the Toll/IL-1 signal transduction pathway 41 2172094CD1 g13569476  7.9E−52 [Mus musculus] immunity-associated nucleotide 4 Daheron, L., et al.(2001) Molecular cloning of Ian4: a BCR/ABL-induced gene that encodes an outer membrane mitochondrial protein with GTP-binding activity. Nucleic Acids Res. 29: 1308-1316 42 7413862CD1 g2117166  4.5E−145 [Homo sapiens] Ras like GTPase 299987|Hs.27453   4E−146 [Homo sapiens] [Hydrolase; GTP-binding protein/GTPase] Member of the Ras superfamily of GTP-binding proteins, has moderate similarity to RAB family GTPases 428226|SEC4L  1.6E−128 [Homo sapiens] [Hydrolase; GTP-binding protein/GTPase; Small molecule- binding protein] Putative GTP-binding protein similar to S. cerevisiae SEC4 299733|  2.3E−95 [Homo sapiens] [Hydrolase; GTP-binding protein/GTPase] Member of the Ras LOC57799 superfamily of GTP-binding proteins, has moderate similarity to RAB family GTPases 329490|Rn.9821  1.3E−35 [Rattus norvegicus] [Hydrolase; GTP-binding protein/GTPase; Small molecule- binding protein] Low molecular weight GTP-binding protein that is expressed in the brain and may have a role in synaptic vesicle transport 344582|MEL  2.8E−35 [Homo sapiens] [Hydrolase; GTP-binding protein/GTPase; Small molecule- binding protein] Protein with similarity to the RAB/YPTand RAS-related proteins; corresponding gene is localized to a region in which translocation breakpoints occur in a number of malignancies 43 7503755CD1 g5020264  8.5E−101 [Mus musculus] Cdc42 GTPase-activating protein Lamarche-Vane, N. and Hall, A. (1998) CdGAP, a novel proline-rich GTPase- activating protein for Cdc42 and Rac. J. Biol. Chem. 273: 29172-29177 611278|Cdgap  7.5E−102 [Mus musculus] [GTPase-activating protein; Activator] Serine-and proline-rich GTPase-activating protein, probably functions in Cdc42 and Rac signaling to bring about actin reorganization 309525|  6.3E−67 [Homo sapiens] [GTPase-activating protein] Protein containing a RhoGAP Hs.169550 domain, has a region of low similarity to murine Mm.4462, which has GTPase- activating activity for the Rac subfamily of ras-related GTP-binding proteins, binds SH3 domains, and inhibits Rac-mediated membrane ruffling 245503|F47A4.3  3.1E−30 [Caenorhabditis elegans] Protein containing a putative breakpoint cluster region (BCR) domain, putative paralog of C. elegans F47A4.4 331736|Rn.11166  3.7E−26 [Rattus norvegicus] [GTPase-activating protein; Activator] N-chimaerin (n- chimerin), ortholog of human CHN1, n-chimerin, which is a GTPase-activating protein for rac (a member of the ras family of GTP-binding proteins), expressed in neurons and developmentally regulated, has a phorbol ester binding domain 334650|CHN1  4.7E−25 [Homo sapiens] [GTPase-activating protein; Activator] Alpha 1 chimerin (chimaerin), a GTPase-activating protein for rac (a member of the ras family of GTP-binding proteins), has divergent SH2 domain at N-terminus but shares C- terminal GTPase-activating domain of alpha 1 chimerin 44 7500488CD1 g12655792  2.1E−148 [Homo sapiens] prune (neural development) protein 372288|  5.8E−20 [Schizosaccharomyces pombe] Putative exopolyphosphatase SPAC2F3.11 10519|PPX1  9.1E−17 [Saccharomyces cerevisiae] [Other phosphatase; Hydrolase] [Cytoplasmic] Exopolyphosphatase, soluble enzyme that degrades polyphosphate chains of all lengths, with a preference for those of 250 residues 45 7510676CD1 g18655335 0.0 [Homo sapiens] epidermal growth factor receptor pathway substrate 8 related protein 3 586475|Eps8  1.6E−51 [Mus musculus][Receptor (signalling)][Nuclear] Epidermal growth factor receptor pathway substrate 8, an adaptor that enhances Egf-induced mitogenesis and mediates PDGF (Pdgfb)-induced Rac1 activation, actin reorganization and membrane ruffling; human EPS8 has a role in neoplastic cell proliferation Maa, M. C. et al. (2001) Overexpression of p97Eps8 leads to cellular transformation: implication of pleckstrin homology domain in p97Eps8-mediated ERK activation. Oncogene 20, 106-12 340492|EPS8  2.7E−51 [Homo sapiens][Receptor (signalling)][Nuclear] Epidermal growth factor receptor pathway substrate 8, SH3 containing protein that is tyrosine phosphorylated by epidermal growth factor receptor (EGFR) and enhances EGF-dependent mitogenic signals, has a role in normal and neoplastic cell proliferation Wong, W. T. et al. (1994) Evolutionary conservation of the EPS8 gene and its mapping to human chromosome 12q23-q24. Oncogene 9, 3057-61

TABLE 3 Poten- tial Gly- SEQ Incyte Amino Potential cosy- ID Polypeptide Acid Phosphorylation lation Analytical Methods NO: ID Residues Sites Sites Signature Sequences, Domains and Motifs and Databases 1 2562907CD1 709 S25 S36 S39 S79 N465 PH domain: L500-P611 HMMER_PFAM S90 S104 S115 S142 S186 S193 S210 S247 S253 S278 S336 S338 S357 S444 S470 S481 S523 S539 S564 S597 S610 S619 S650 S685 T176 T595 T632 T698 T701 RhoGEF domain: A287-A466 HMMER_PFAM SH3 domain: R631-I681 HMMER_PFAM PROTEIN NEUROBLASTOMA PROBABLE BLAST_PRODOM GUANINE NUCLEOTIDE REGULATORY TIM ONCOGENE P60 PD152413: M471-L606 PROTEIN FACTOR GUANINE-NUCLEOTIDE BLAST_PRODOM RELEASING NUCLEOTIDE GUANINE EXCHANGE PROTO-ONCOGENE BINDING SH3 PD000777: E290-N465 PROBABLE GUANINE NUCLEOTIDE BLAST_PRODOM REGULATORY PROTEIN TIM ONCOGENE P60 TRANSFORMING IMMORTALIZED MAMMARY GUANINE-NUCLEOTIDE RELEASING FACTOR PROTO-ONCOGENE SH3 DOMAIN PD115468: R190-E286 2 3744219CD1 558 S20 S198 S243 N93 signal_cleavage: M1-S51 SPSCAN S260 S279 S280 N265 S284 S338 S390 S411 S540 T121 T207 T292 T323 T381 T394 T491 T496 LGN motif, putative GEF specific for G-alpha: I499-L521 HMMER_PFAM Raf-like Ras-binding domain: K302-R373, T375-L445 HMMER_PFAM Regulator of G protein signaling domain: S67-L184 HMMER_PFAM Regulator of G protein signaling domain PF00615: BLIMPS_PFAM F84-C100, I162-V175 REGULATOR OF G-PROTEIN SIGNALING BLAST_PRODOM SIGNAL TRANSDUCTION INHIBITOR ALTERNATIVE PD016903: K352-P477, S488-E543, A318-Q351 REGULATOR OF SIGNALING G-PROTEIN BLAST_PRODOM SIGNAL TRANSDUCTION INHIBITOR RGS12 PROTEIN PD013247: L185-Q351 REGULATOR OF G-PROTEIN SIGNALING BLAST_PRODOM RGS14 SIGNAL TRANSDUCTION INHIBITOR RAP1/RAP2 INTERACTING PD033865: M1-A65 RECEPTOR KINASE G-PROTEIN SIGNAL BLAST_PRODOM TRANSDUCTION INHIBITOR REGULATOR OF SIGNALING G PD001580: S67-L184 RGS DOMAIN DM01609| BLAST_DOMO P49798|20-186: E58-Y180 |P49808|1-167: G34-R181 |P41220|42-207: P53-E182 |P49796|353-518: P55-L193 3 5515030CD1 414 S58 S123 S308 N79 WD domain, G-beta repeat: C336-D372, C169-D205, HMMER_PFAM S364 T115 T158 N101 C378-R414, C294-S330, E210-D246, E126-S163, T166 T172 T200 N227 K252-D288, L84-D120 T213 T228 T249 T283 T299 T313 T325 T333 T367 T409 Trp-Asp (WD-40) repeat protein BL00678: T277-W287 BLIMPS_BLOCKS Trp-Asp (WD-40) repeats signature: V181-F226, PROFILESCAN I222-N269, S348-N395, S264-D311, N97-F142 Trp-Asp (WD) repeats signature: V192-I206, I233-A247, MOTIFS I275-A289, L359-A373 4 1681532CD1 623 S19 S23 S31 S174 PH domain: D114-A190, D252-H329 HMMER_PFAM S206 S226 S313 S350 S372 S378 S401 S418 S451 S478 S533 S549 S566 S583 T220 T306 T328 T361 T411 T483 Y183 Y592 PROTEIN PAK-INTERACTING EXCHANGE BLAST_PRODOM FACTOR BETA SH3 DOMAIN PD150837: Q69-K187 (P value = 3.9e−10) Leucine zipper pattern: L164-L185, L171-L192 MOTIFS 5 70845770CD1  226 S67 S132 T71 T73 signal_cleavage: M1-A14 SPSCAN CYCLIN CELL CYCLE DIVISION PD02331: R93-R139, BLIMPS_PRODOM N174-V206 6 3448184CD1 1849 S75 S170 S310 N149 DENN (AEX-3) domain: L159-G298 HMMER_PFAM S418 S535 S623 N1033 S624 S642 S687 N1251 S792 S801 S862 N1301 S1035 S1085 S1101 N1402 S1104 S1130 S1133 N1573 N1716 N1743 S1143 S1221 S1227 PH domain: R1744-S1847 HMMER_PFAM S1269 S1273 S1282 S1352 S1454 S1506 S1516 S1561 S1576 S1619 S1644 S1680 S1710 S1738 HYDROLASE PROTEIN MYOTUBULARIN BLAST_PRODOM S1779 S1784 S1811 DISEASE MUTATION F53A2.8 S1821 T71 T84 PROTEINTYROSINE PHOSPHATASE C19A8.03 T95 T299 T519 CPA2NNF1 PD014611: F1283-R1456, K1452-R1520, T568 T712 T731 D1117-Q1216, G916-L979 T763 T922 T930 T957 T1065 PROTEIN REGULATOR OF PRESYNAPTIC BLAST_PRODOM T1067 T1097 ACTIVITY SERINE PROTEASE INHIBITOR T1255 T1367 RAB3 GDP/GTP PD008900: L152-L327, R3-G108, T1488 T1525 L351-R396, G1759-S1779 T1600 T1634 T1677 T1737 T1820 Y708 Y1751 7 6322968CD1 322 S16 S104 S123 N97 DOCK180 PROTEIN PD146574: Y89-S282 BLAST_PRODOM S151 S162 S171 N137 S282 T24 T99 N285 T118 T210 T246 Y89 PROTEIN DOCA MYOBLAST CITY DOCK180 BLAST_PRODOM CED5 C02F4.1 CHROMOSOME XII COSMID PD011906: M1-K87 8 6819485CD1 775 S40 S53 S61 S143 N212 PDZ domain (Also known as DHR or GLGF).: E136-P220 HMMER_PFAM S206 S231 S242 N398 S292 S299 S317 S391 S445 S469 S482 S574 S683 S707 S720 S730 T72 T156 T293 T356 T667 T668 T734 T748 Y134 Y572 Y641 Cell attachment sequence: R57-D59 MOTIFS PDZ domain proteins PF00595 I181-N191 BLIMPS_PFAM Protein SH3 domain repeat PD00289 G184-N197 BLIMPS_PRODOM PPGPP GTP Pyrophosphokin PD002296 K658-E686 BLIMPS_PRODOM 9 7499882CD1 438 S5 S41 S90 S205 N19 EPIDERMAL GROWTH FACTOR RECEPTOR BLAST_PRODOM S214 S230 S231 KINASE SUBSTRATE EPS8 SH3 DOMAIN S264 S309 S355 PHOSPHORYLATION PD011987: Q28-G158 S372 S410 T36 T84 T115 T263 T343 T371 T377 T387 T416 10 6623259CD1 316 S30 S58 S171 S237 N56 signal_cleavage: M1-S24 SPSCAN S241 T20 T108 N263 T155 T196 T204 T254 T265 11 2239208CD1 1019 S68 S169 S283 N83 RhoGAP domain: P614-A777 HMMER_PFAM S305 S414 S425 S434 S470 S508 S563 S664 S719 S861 S956 S994 T14 T128 T164 Phorbol esters/diacylglycerol binding domain: H543-C586 HMMER_PFAM T178 T235 T360 T504 T565 T734 T870 T989 Phorbol esters/diacylglycerol binding domain BLIMPS_BLOCKS proteins BL00479: Q541-S563, S563-C578 PTPL1-ASSOCIATED RHOGAP PD146000: L348-V613 BLAST_PRODOM PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM ZINC 3-KINASE SH3 PHOSPHATIDYL INOSITOL REGULATORY PD000780: V613-D772 ZK669.1 PROTEIN ALTERNATIVE SPLICING BLAST_PRODOM PD182724 K233-A405, L437-V600, D852-S898 PTPL1-ASSOCIATED RHOGAP ZK669.1 BLAST_PRODOM PROTEIN ALTERNATIVE SPLICING PD156019: E131-T218 PH DOMAIN DM00470 BLAST_DOMO |Q03070|63-292: M561-I799 |P52757|241-463: C567-I799 |A43953|74-296: E566-I799 |P15882|109-331: E566-I799 Aldehyde dehydrogenases glutamic acid active site: MOTIFS V658-P665 Phorbol esters/diacylglycerol binding domain: MOTIFS H543-C586 12 3821431CD1 490 S9 S94 S129 S175 N197 S229 S281 S282 N260 S286 S291 S304 N289 S340 S373 S407 N335 S416 S448 S460 N352 T18 T48 T56 T209 N474 T250 T316 T348 T399 T401 T482 Y58 Y192 13 6973721CD1 386 S206 S239 S287 N264 signal_cleavage: M1-A29 SPSCAN S358 Signal Peptide: M1-A29, M1-C31 HMMER 14 7499694CD1 465 S9 S104 S150 S204 N172 S256 S257 S261 N235 S266 S279 S315 N264 S348 S382 S391 N310 S423 S435 T18 T48 N327 T56 T184 T225 N449 T291 T323 T374 T376 T457 Y58 Y167 15 2454570CD1 917 S12 S111 S114 N128 PDZ domain (Also known as DHR or GLGF): Q18-M94 HMMER_PFAM S337 S344 S393 S449 S461 S554 S585 S595 S636 S649 S655 S684 S726 S738 S743 S778 S914 T208 T237 T318 T402 T621 T660 T700 T730 T782 Y16 Regulator of G protein signaling domain: S792-I908, HMMER_PFAM L365-E784 Regulator of G protein signaling domain: PF00615: BLIMPS_PFAM S738-K744, I886-L899, F809-C825 REGULATOR OF GPROTEIN SIGNALING 3 BLAST_PRODOM RGS3 RGP3 SIGNAL TRANSDUCTION INHIBITOR PD096072: T621-H722 REGULATOR OF GPROTEIN SIGNALING 3 BLAST_PRODOM RGS3 RGP3 SIGNAL TRANSDUCTION INHIBITOR PD178959: E506-S595 SIGNAL MULTIPLE BANDED ANTIGEN BLAST_PRODOM PRECURSOR REGULATOR OF GPROTEIN SIGNALING RGS3 PD155675: E421-Q505, K445-Q540, D476-K546, Q439-Q523, P418-Q493 RECEPTOR KINASE GPROTEIN SIGNAL BLAST_PRODOM TRANSDUCTION INHIBITOR REGULATOR OF SIGNALING G PD001580: S792-I908 RGS DOMAIN DM01609 BLAST_DOMO P49796|353-518: K751-L917 |P41220|42-207: K751-S914 |P49798|20-186: K751-N909 |Q08116|38-195: M776-N909 ATP/GTP-binding site motif A (P-loop): G214-S221 MOTIFS 16 6595652CD1 606 S28 S66 S76 S96 N10 RANBP3 PROTEIN ALTERNATIVE SPLICING BLAST_PRODOM S139 S147 S172 N72 PD181787: E46-D320 S200 S258 S283 N277 S315 S344 S357 N281 S367 S392 S397 N313 S407 S456 S472 N348 S489 S508 S511 N365 S532 S552 S572 S578 T419 T432 T515 RANBP3 PROTEIN ALTERNATIVE SPLICING BLAST_PRODOM PD172268: I512-T606 RANBP3 PROTEIN ALTERNATIVE SPLICING BLAST_PRODOM PD179958: S345-V428 ACTIVATING; RAN; GTPASE; ISOZYME; BLAST_DOMO DM01269|P40517|202-326: K427-Y540 17 5770223CD1 377 S88 S106 S116 PROTEIN DIAPHANOUS HOMOLOG CELL BLAST_PRODOM S168 S264 S282 DIVISION COILED COIL P140MDIA DIA12C S313 S373 T95 DIA156 PD005957: E253-D329 T311 18 7729840CD1 874 S11 S63 S86 S138 N52 PH domain: W266-A368 HMMER_PFAM S143 S152 S158 N150 S241 S301 S308 N430 S317 S383 S434 N450 N645 N747 S437 S591 S603 RhoGAP domain: F397-T547 HMMER_PFAM S624 S687 S688 S709 S734 S737 S742 S811 S817 S826 T32 T77 T165 SH3 domain: R819-L874 HMMER_PFAM T242 T332 T470 T574 T647 T682 T693 T695 T765 Y141 Y142 Y488 OLIGOPHRENIN RHOGAP PROTEIN CODED BLAST_PRODOM FOR BY C ELEGANS CDNA YK129F4.5 PD023026: F194-F395 OLIGOPHRENIN CODED BY C ELEGANS CDNA BLAST_PRODOM PD023027: L6-K193 PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM ZINC 3-KINASE SH3 PHOSPHATIDYLINOSITOL REGULATORY PD000780: V398-E546 OLIGOPHRENIN 1 PD117931: T547-R819 BLAST_PRODOM PH DOMAIN DM00470 BLAST_DOMO |A43953|74-296: V398-H567 |P15882|109-331: V398-H567 |Q03070|63-292: C401-H567 |P52757|241-463: C401-H567 19 4635167CD1 335 S110 S215 S224 signal_cleavage: M1-A54 SPSCAN S332 T26 T33 T57 T116 T314 PH domain: F228-S331 HMMER_PFAM RhoGEF domain: T26-T196 HMMER_PFAM Guanine-nucleotide dissociation stimulators CDC24 BLIMPS_BLOCKS family signature BL00741: E32-L41, L145-A167 VAV; KINASE; ZINC; SH2 DM08580|P52735|1-491: BLAST_DOMO K22-K259 20 7499571CD1 849 S39 S50 S88 S141 N459 Formin Homology 2 Domain: P373-D814 HMMER_PFAM S382 S441 S466 N600 S696 S730 S833 T87 T164 T168 T217 T263 T562 T791 T819 Y155 Y410 PROTEIN DEVELOPMENTAL FORMIN LIMB BLAST_PRODOM DEFORMITY NUCLEAR ALTERNATIVE SPLICING CELL DIAPHANOUS PD003542: V550-N801 DIAPHANOUS CELL DIVISION COILED COIL BLAST_PRODOM PD + F92005957: L48-D215, M1-F60 DIAPHANOUS FORMIN LIMB DEFORMITY BLAST_PRODOM NUCLEAR DEVELOPMENTAL ALTERNATIVE SPLICING EST PD004159: N360-E548 DIAPHANOUS CELL DIVISION COILED COIL BLAST_PRODOM PD042786: D213-A279 FORMIN DM04565 BLAST_DOMO |Q05859|5-1205: P298-L786, L226-F288, G121-A154 |Q05858|1-1212: P298-L786, E254-P315, V76-D136 |Q05860|176-1467: P298-K763, D259-P373, E642-L786 REGULATORY DM05091|S54986|1-980: L85-Q282, BLAST_DOMO P326-F741, P298-I491, I749-K790 21 8047234CD1 1765 S4 S21 S26 S177 N432 GRIP domain: S1705-V1752 HMMER_PFAM S199 S223 S248 N728 S268 S395 S470 N765 S531 S621 S673 N831 S700 S741 S767 N942 S792 S832 S850 N1015 S902 S908 S952 N1292 N1309 N1561 N1580 N1619 N1632 N1759 S1004 S1123 S1125 RanBP1 domain.: E1048-L1169, E1345-A1466 HMMER_PFAM S1132 S1137 S1294 S1347 S1348 S1358 S1455 S1517 S1523 S1544 S1551 S1590 S1594 S1607 S1726 TPR Domain: P60-Q93 HMMER_PFAM S1742 T76 T92 T178 T210 T231 T282 T469 T526 T562 T669 T970 T978 T1016 T1051 T1184 T1216 RanBP1 domain proteins PF00638: W1076-E1090 BLIMPS_PFAM T1234 T1317 T1324 T1422 T1429 T1465 T1482 T1499 T1528 T1634 T1650 T1661 Y11 Y42 NUCLEAR PORE COMPLEX NUCLEOPORIN BLAST_PRODOM RAN-BINDING 2 TRANSPORT REPEAT ZINC FINGER ISOMERASE ROTAMASE PD044178: E192-G900, L889-V1047, E1326-V1344 NUCLEAR PORE COMPLEX PROTEIN BLAST_PRODOM NUCLEOPORIN RAN-BINDING TRANSPORT REPEAT PD023309: T1465-K1640 PD020903: M1197-V1344 CHROMOSOME III COILED COIL PD023308: BLAST_PRODOM W1645-N1759 ACTIVATING; RAN; GTPASE; ISOZYME BLAST_DOMO DM01269 |P49792|2319-2441: L1343-A1466, V1047-Q1167 |P49792|2021-2144: E1045-L1169, V1344-K1464 |P49792|2919-3056: V1344-S1478, P1044-H1179 |P49792|1181-1303: K1046-L1169, V1344-T1465 Leucine zipper pattern: L451-L472, L576-L597 MOTIFS 22 8217739CD1 1041 S60 S81 S97 S136 N58 PH domain: L622-N721 HMMER_PFAM S226 S230 S278 N242 S335 S356 S580 N1033 S590 S591 S615 S627 S636 S740 S777 S806 S817 S861 S881 S890 S911 S936 S954 S987 S1000 T92 T106 T115 RhoGEF domain: A377-A564 HMMER_PFAM T368 T501 T897 T1019 T1037 Y717 SIMILAR TO HUMAN VAV GENE PRODUCT BLAST_PRODOM PD184978: R572-S787, D803-P898 PROTEIN FACTOR GUANINENUCLEOTIDE BLAST_PRODOM RELEASING NUCLEOTIDE GUANINE EXCHANGE PROTOONCOGENE BINDING SH3 PD000777: E380-N563 23  413973CD1 175 T57 T117 Leucine Rich Repeat: N107-T129, R130-A152 HMMER_PFAM Leucine-rich repeat signature PR00019: L108-I121, BLIMPS_PRINTS L128-I141 24 7501022CD1 1024 S66 S234 S242 N18 signal_cleavage: M1-F59 SPSCAN S251 S335 S413 N498 S420 S492 S661 S670 S676 S685 S712 S769 S789 S799 S827 S921 S937 S983 S992 S1015 T57 T151 T166 T197 T272 T377 T485 T511 Y266 Y914 PH domain: N387-H482, P44-L145 HMMER_PFAM RHO-INTERACTING P116RIP RIP3 GUANINE- BLAST_PRODOM NUCLEOTIDE RELEASING FACTOR COILED PD122130: E280-E532 P116 RHO-INTERACTING PROTEIN P116RIP BLAST_PRODOM RIP3 GUANINENUCLEOTIDE RELEASING FACTOR COILED COIL PD033992: G883-D1023 PD185384: R533-L677 PD185383: Q156-A278 TRICHOHYALIN DM03839 BLAST_DOMO |P22793|921-1475: R509-Q964 |P37709|632-1103: R548-E970 25  182852CD1 1143 S66 S235 S243 N18 PH domain: N506-H601, P44-L145 HMMER_PFAM S252 S301 S332 N617 S348 S382 S419 S454 S532 S539 S611 S780 S789 S795 S804 S831 S888 S908 S918 S946 S1040 S1056 S1102 S1111 S1134 T57 T151 T166 T198 T273 T354 T371 T496 T604 T630 Y267 Y1033 RHO-INTERACTING P116RIP RIP3 GUANINE BLAST_PRODOM NUCLEOTIDE RELEASING FACTOR COILED PD122130: R417-E651, E281-P303 P116 RHO-INTERACTING PROTEIN P116RIP BLAST_PRODOM RIP3 GUANINE-NUCLEOTIDE-RELEASING FACTOR COILED COIL PD033992: G1002-D1142 PD185384: R652-L796 PD185383: Q156-A279 TRICHOHYALIN DM03839 BLAST_DOMO |P22793|921-1475: R628-Q1083 |P37709|632-1103: R667-E1089 26 1644979CD1 1154 S2 S72 S85 S186 N49 Formin Homology 2 Domain: H459-K893 HMMER_PFAM S270 S343 S367 N375 S458 S493 S505 N1145 S556 S716 S760 S762 S810 S931 S982 S1031 PROTEIN DEVELOPMENTAL FORMIN LIMB BLAST_PRODOM S1032 S1052 S1088 DEFORMITY NUCLEAR ALTERNATIVE S1097 S1132 S1134 SPLICING CELL DIAPHANOUS PD003542: T304 T333 T378 L636-P869 T466 T536 T569 T570 FORMIN DM04565 BLAST_DOMO T655 T755 T771 Q05858|1-1212: P421-T814, F279-P433, K17-L78 T817 T894 T945 |Q05860|5-1205: A413-T814, E336-G437 T992 T1009 T1084 |Q05860|176-1467: A413-E860, E336-G437 T1092 T1123 T1147 Y801 REGULATORY; DM05091|S54986|1-980: P421-R827, BLAST_DOMO P208-V319 Cell attachment sequence: R898-D900 MOTIFS Aminoacyl transfer RNA synthetases class-II MOTIFS signature 2: F504-F513 Alkaline phosphatase active site: V1103-T1111 MOTIFS 27 55111748CD1  1123 S3 S78 S89 S107 N49 SH3 domain: G701-1757, R627-L681, F1065-L1121 HMMER_PFAM S108 S116 S143 S202 S203 S209 S240 S246 S254 S292 S296 S310 S315 S337 S340 S342 S365 Sorbin homologous domain: V244-D289 HMMER_PFAM S387 S403 S496 S515 S534 S538 S544 S556 S622 S718 S804 S855 S870 S872 S946 S977 Src homology 3 (SH3) domain proteins profile BLIMPS_BLOCKS S1019 S1104 T46 BL50002: A631-D649, T1107-P1120 T57 T66 T72 T265 T356 T419 T433 T444 T504 T593 T617 T639 T676 T693 SH3 domain signature PR00452: D732-P741, R627-A637, BLIMPS_PRINTS T713 T743 T752 V715-Q730 T876 T1002 T1024 T1054 T1060 T1103 Y291 Y316 Y359 Y662 Y736 Neutrophil cytosol factor 2 signature PR00499: BLIMPS_PRINTS D649-E665, E665-I678 SH3 DOMAIN-CONTAINING PROTEIN SH3P12 BLAST_PRODOM SH3 DOMAIN REPEAT PD113253: K45-1260 SH3 DOMAIN-CONTAINING PROTEIN SH3P12 BLAST_PRODOM SH3 DOMAIN REPEAT PD085493: S467-E569 PROTEIN SH3 SH3-CONTAINING P4015 BLAST_PRODOM ARG/ABL-INTERACTING ARGBP2A SORBIN DOMAIN-CONTAINING SH3P12 DOMAIN PD016158: M275-K381, P412-E429 28 3358362CD1 591 S16 S27 S36 S43 N206 PH domain: L376-G502 HMMER_PFAM S52 S53 S112 S154 N449 S214 S244 S272 S278 S282 S320 S358 S372 S393 S397 S417 S427 S488 S501 RhoGEF domain: A163-E342 HMMER_PFAM T196 T198 T316 T396 T413 T486 T512 T521 Y323 Y385 Y421 Y547 SH3 domain: E515-I568 HMMER_PFAM Neutrophil cytosol factor 2 signature PR00499: BLIMPS_PRINTS V514-D534, D534-E550 PROTEIN K07D4.7 NEUROBLASTOMA BLAST_PRODOM PROBABLE GUANINE NUCLEOTIDE REGULATORY TIM ONCOGENE P60 PD152413: M347-L497 PROTEIN FACTOR GUANINENUCLEOTIDE BLAST_PRODOM RELEASING NUCLEOTIDE GUANINE EXCHANGE PROTOONCOGENE BINDING SH3 PD000777: E166-E342 RHO1 GDP-GTP EXCHANGE PROTEIN BLAST_DOMO DM07085|P51862|155-1355: R135-A484 29 8113230CD1 1062 S80 S111 S136 N251 Fes/CIP4 homology domain: K22-Y121 HMMER_PFAM S214 S236 S294 N856 S313 S410 S485 N897 S523 S546 S716 S735 S740 S788 S806 S812 S857 S899 RhoGAP domain: P497-Q649 HMMER_PFAM S903 S1007 T116 T293 T368 T380 T386 T392 T414 T466 T478 T701 T715 T782 T814 SH3 domain: I723-Q777 HMMER_PFAM T916 T958 T981 T1005 T1014 T1056 Y63 Y87 Y682 SH3 domain signature PR00452: I723-G733, R737-R752, BLIMPS_PRINTS S754-N763, I765-Q777 F12F6.5 RHOGAP HEMATOPOIETIC PROTEIN BLAST_PRODOM C1 P115 KIAA0131 GTPASE ACTIVATION SH3 PD042850: E134-G470 PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM ZINC 3KINASE SH3 PHOSPHATIDYLINOSITOL REGULATORY PD000780: V495-E645 PH DOMAIN DM00470 BLAST_DOMO |P98171|405-693: R406-I670 |Q03070|63-292: P497-I670 |P52757|241-463: P497-I670 |P15882|109-331: P497-I670 30 1785616CD1 1185 S3 S18 S62 S84 N491 PH domain: E29-K78 HMMER_PFAM S158 S298 S362 N531 S427 S497 S524 N620 S533 S594 S621 N680 S665 S684 S825 N698 S847 S855 S865 S993 S1028 S1032 S1046 S1054 S1067 S1086 T122 T285 T475 T496 T670 T860 T1072 Y169 Y190 GTPase-activator protein for Ras-like GTPase: F291-F492 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN V382-L481 GAP24 PD142012: S3-F291 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: L282-N491 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490 |B40121|268-786: R443-E510, K221-K357, V36-Y190 |P09851|442-960: R443-E510, V36-Y190, K221-K357 EGGSHELL; DM05294|C44805|1-194: G890-T989 BLAST_DOMO 31 71113255CD1  1101 S12 S29 S39 S72 N189 RhoGAP domain: P34-S186 HMMER_PFAM S221 S240 S283 N362 S298 S317 S349 N437 S401 S402 S489 S511 S517 S519 S542 S576 S611 S709 S883 S988 S1043 S1048 S1082 T107 T209 T271 T302 T321 T382 T388 T681 T860 T974 T1020 Y807 PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM ZINC 3-KINASE SH3 PHOSPHATIDYL INOSITOL REGULATORY PD000780: V33-A185 PROTEIN REPEAT TROPOMYOSIN COILED BLAST_PRODOM COIL ALTERNATIVE SPLICING SIGNAL PRECURSOR CHAIN PD000023: I671-E863, E673-A851 PROTEIN COILED COIL CHAIN MYOSIN BLAST_PRODOM REPEAT HEAVY ATP-BINDING FILAMENT HEPTAD PD000002: Q699-Q903 PH DOMAIN BLAST_DOMO DM00470|A49307|566-842: S3-H210 DM00470|P15882|109-331: E15-D212 DM00470|A43953|74-296: E15-D212 DM00470|Q03070|63-292: E15-D212 32 7502098CD1 1308 S22 S61 S90 S94 N649 PH domain: E187-K236 HMMER_PFAM S119 S125 S140 N689 S161 S176 S220 N778 S242 S316 S456 N838 S520 S585 S655 N856 S682 S691 S752 S779 S823 S842 S983 S1005 S1013 S1023 S1151 S1186 S1190 S1204 S1212 S1225 S1244 T280 T443 T633 T654 T828 T1018 T1230 Y85 Y327 Y348 GTPase-activator protein for Ras-like GTPase: F449-F650 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN V540-L639 GAP24 PD142012: D25-F449 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: L440-N649 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490 |B40121|268-786: R601-E668, K379-K515, V194-Y348 |P09851|442-960: R601-E668, V194-Y348, K379-K515 EGGSHELL; DM05294|C44805|1-194: G1048-T1147 BLAST_DOMO 33 7502099CD1 1279 S22 S61 S90 S94 N620 PH domain: E187-K236 HMMER_PFAM S119 S125 S140 N660 S161 S176 S220 N749 S242 S316 S456 N809 S520 S556 S626 N827 S653 S662 S723 S750 S794 S813 S954 S976 S984 S994 S1122 S1157 S1161 S1175 S1183 S1196 S1215 T280 T443 T604 T625 T799 T989 T1201 Y85 Y327 Y348 GTPase-activator protein for Ras-like GTPase: F449-F621 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN R484-L610 GAP24 PD142012: D25-F449 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: S520-N620, L440-A526 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490|B40121|268-786: K379-E639, V194-Y348 DM08490|P09851|442-960: K379-E639, V194-Y348 EGGSHELL; DM05294|C44805|1-194: G1019-T1118 BLAST_DOMO 34 7502100CD1 1293 S22 S61 S90 S94 N620 PH domain: E187-K236 HMMER_PFAM S119 S125 S140 N660 S161 S176 S220 N749 S242 S316 S456 N763 S520 S556 S626 N823 S653 S662 S723 N841 S750 S764 S808 S827 S968 S990 S998 S1008 S1136 S1171 S1175 S1189 S1197 S1210 S1229 T280 T443 T604 T625 T813 T1003 T1215 Y85 Y327 Y348 GTPase-activator protein for Ras-like GTPase: F449-F621 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN R484-L610 GAP24 PD142012: D25-F449 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: S520-N620, L440-A526 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490 |B40121|268-786: K379-E639, V194-Y348 |P09851|442-960: K379-E639, V1947-Y348 EGGSHELL; DM05294|C44805|1-194: G1033-T1132 BLAST_DOMO 35 7502750CD1 1199 S3 S18 S62 S84 N491 PH domain: E29-K78 HMMER_PFAM S158 S298 S362 N531 S427 S497 S524 N620 S533 S594 S621 N634 S635 S679 S698 N694 S839 S861 S869 N712 S879 S1007 S1042 S1046 S1060 S1068 S1081 S1100 T122 T285 T475 T496 T684 T874 T1086 Y169 Y190 GTPase-activator protein for Ras-like GTPase: F291-F492 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN V382-L481 GAP24 PD142012: S3-F291 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: L282-N491 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490 |B40121|268-786: R443-E510, K221-K357, V36-Y190 |P09851|442-960: R443-E510, V36-Y190, K221-K357 EGGSHELL; DM05294|C44805|1-194: G904-T1003 BLAST_DOMO 36 7502891CD1 1170 S3 S18 S62 S84 N462 PH domain: E29-K78 HMMER_PFAM S158 S298 S362 N502 S398 S468 S495 N591 S504 S565 S592 N605 S606 S650 S669 N665 S810 S832 S840 N683 S850 S978 S1013 S1017 S1031 S1039 S1052 S1071 T122 T285 T446 T467 T655 T845 T1057 Y169 Y190 GTPase-activator protein for Ras-like GTPase: F291-F463 HMMER_PFAM Ras GTPase-activating proteins signature and profile: PROFILESCAN R326-L452 GAP24 PD142012: S3-F291 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INHIBITORY REGULATOR PD002301: S362-N462 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490|B40121|268-786: K221-E481, V36-Y190 DM08490|P09851|442-960: K221-E481, V36-Y190 EGGSHELL; DM05294|C44805|1-194: G875-T974 BLAST_DOMO 37 2571532CD1 397 S84 S192 S236 N90 PDZ domain (Also known as DHR or GLGF).: V101-G190 HMMER_PFAM S243 S335 S374 N109 S389 T2 T151 N387 T208 Y286 Protein SH3 domain repeat PD00289 G153-G166 BLIMPS_PRODOM CYTOHESIN BINDING PROTEIN HE BLAST_PRODOM TRANSCRIPTION FACTOR PD036719: T187-L264, L330-Q396 GLGF DOMAIN DM00224|S43424|32-127: L91-L188 BLAST_DOMO 38 6436087CD1 307 S43 S44 S51 S56 RhoGAP domain: P129-S281 HMMER_PFAM S101 T98 T239 PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM ZINC 3-KINASE SH3 PHOSPHATIDYL INOSITOL REGULATORY PD000780: V128-T280 PH DOMAIN DM00470 BLAST_DOMO |P46941|504-803: K88-L272 |P15882|109-331: Y107-Q298 |A49307|566-842: L78-T285 |P11274|973-1254: E35-P283 39 7502109CD1 1322 S22 S61 S90 S94 N649 PH domain: E187-K236 HMMER_PFAM S119 S125 S140 N689 S161 S176 S220 N778 S242 S316 S456 N792 S520 S585 S655 N852 N870 S682 S691 S752 GTPase-activator protein for Ras-like GTPase: F449-F650 HMMER_PFAM S779 S793 S837 S856 S997 S1019 S1027 S1037 S1165 S1200 S1204 S1218 S1226 S1239 S1258 Ras GTPase-activating proteins signature and profile: PROFILESCAN T280 T443 T633 V540-L639 T654 T842 T1032 T1244 Y85 Y327 Y348 GAP24 PD142012: D25-F449 BLAST_PRODOM PROTEIN GTPASE ACTIVATION GTPASE- BLAST_PRODOM ACTIVATING RAS NEUROFIBROMIN P21 ACTIVATOR INFHIBITORY REGULATOR PD002301: L440-N649 RAS-SPECIFIC GAP CATALYTIC DOMAIN BLAST_DOMO DM08490 |B40121|268-786: R601-E668, V194-Y348, K379-K515 |P09851|442-960: R601-E668, V194-Y348, K379-K515 EGGSHELL; DM05294|C44805|1-194: G1062-T1161 BLAST_DOMO 40 7500262CD1 217 S125 S182 T106 Signal_cleavage: M1-L25 SPSCAN Signal Peptide: M1-G18 HMMER 41 2172094CD1 306 S22 S26 S70 S92 Signal_cleavage: M1-S41 SPSCAN S161 S167 S261 S270 S273 S297 T8 T27 T125 T152 T193 Cytosolic domain: H293-D306 TMHMMER Transmembrane domain: S273-L292 Non-cytosolic domain: M1-R272 IMMUNITY-ASSOCIATED PROTEIN, 38 KDA BLAST_PRODOM IMMUNE ASSOCIATED PROTEIN 38 PD119787: R101-R295 ATP/GTP-binding site motif A (P-loop): G34-S41 MOTIFS 42 7413862CD1 309 S7 S65 S198 S223 N5 Ras family: K48-V233 HMMER_PFAM S305 T19 T183 N300 T249 T280 GTP-binding nuclear protein ran proteins BLIMPS_BLOCKS BL01115: L47-L90, D127-R170, E178-L208 Transforming protein P21 RAS signature BLIMPS_PRINTS PR00449: P149-L162, F184-V206, L47-D68, I88-T110 RAS LIKE GTPASE RAR GTP-BINDING BLAST_PRODOM PROTEIN PD029955: H210-S309 PROTEIN GTP-BINDING LIPOPROTEIN BLAST_PRODOM PRENYLATION TRANSPORT RAS-RELATED FAMILY MULTIGENE ADP RIBOSYLATION SUBUNIT PD000015: F45-R159, K165-R204 RAS TRANSFORMING PROTEIN DM00006 BLAST_DOMO P28186|12-158: Y43-E186 P24407|5-150: Y43-E186 P17609|6-151: Y43-E186 P24409|6-151: Y43-E186 ATP/GTP-binding site motif A (P-loop): G53-S60 MOTIFS 43 7503755CD1 1044 S12 S29 S39 S72 N5 RhoGAP domain: P34-S186 HMMER_PFAM S221 S240 S283 N300 S298 S317 S349 N189 S401 S402 S489 N362 S519 S554 S652 N437 S826 S931 S986 S991 PROTEIN GTPASE DOMAIN SH2 ACTIVATION BLAST_PRODOM S1025 T107 T209 ZINC 3-KINASE SH3 PHOSPHATIDYL INOSITOL T271 T302 T321 REGULATORY PD000780: V33-A185 T382 T388 T624 T803 T917 T963 Y750 PROTEIN REPEAT TROPOMYOSIN COILED BLAST_PRODOM COIL ALTERNATIVE SPLICING SIGNAL PRECURSOR CHAIN PD000023: I614-E806, E616-A794 PROTEIN COILED COIL CHAIN MYOSIN BLAST_PRODOM REPEAT HEAVY ATP-BINDING FILAMENT HEPTAD PD000002: Q642-Q846 PH DOMAIN DM00470| BLAST_DOMO A49307|566-842: S3-H210 P15882|109-331: E15-D212 A43953|74-296: E15-D212 Q03070|63-292: E15-D212 44 7500488CD1 400 S111 S294 S312 Signal_cleavage: M1-A48 SPSCAN S346 S361 S398 T46 T115 T153 T191 DHHA2 domain: F215-L306 HMMER_PFAM PRUNE EXOPOLYPHOSPHATASE BLAST_PRODOM METAPHOSPHATASE PROTEIN HYDROLASE GENE PUTATIVE XPP PD011764: E50-G245, R16-E154, K236-L306 Leucine zipper pattern: L157-L178, L164-L185 MOTIFS Cell attachment sequence: R66-D68 MOTIFS 45 7510676CD1 422 S5 S41 S90 S205 N19 EPIDERMAL GROWTH FACTOR RECEPTOR BLAST_PRODOM S214 S230 S231 KINASE SUBSTRATE EPS8 SH3 DOMAIN S264 S309 S355 PHOSPHORYLATION S372 S410 T36 T84 PD011987: Q28-G158, E236-K268, R265-T371 T115 T263 T343 T371 T377 T387

TABLE 4 Polynucleotide SEQ ID NO:/ Incyte ID/Sequence Length Sequence Fragments 46/2562907CB1/ 1-469, 115-2556, 229-248, 274-901, 275-506, 287-976, 322-463, 441-1175, 456-1209, 560-777, 625-1021, 756-885, 2877 793-1458, 960-1357, 1069-1387, 1104-1740, 1104-1747, 1127-1746, 1163-1754, 1196-1532, 1220-1748, 1232- 1479, 1234-1505, 1290-1535, 1336-1880, 1385-2045, 1405-1791, 1426-1692, 1439-2063, 1549-1923, 1588-1857, 1603-1862, 1603-2000, 1603-2065, 1622-2249, 1659-1934, 1686-1984, 1691-2081, 1706-1803, 1740-2227, 1745- 1866, 1758-2353, 1802-1923, 1808-2448, 1848-2370, 1849-2069, 1871-2475, 1873-2463, 1892-2213, 1894-2457, 1905-2521, 1924-2498, 1930-2470, 1931-2565, 1940-2426, 1944-2351, 1950-2456, 1968-2442, 1976-2405, 1993- 2615, 2014-2567, 2035-2293, 2060-2684, 2073-2676, 2091-2318, 2109-2720, 2111-2720, 2114-2709, 2150-2781, 2161-2759, 2214-2708, 2220-2877, 2234-2807, 2241-2814, 2271-2516, 2324-2556, 2327-2581, 2345-2775 47/3744219CB1/ 1-594, 121-623, 407-1097, 420-1954, 435-889, 458-959, 495-771, 496-771, 535-990, 535-1135, 570-909, 571-724, 2270 743-1166, 765-1045, 834-1101, 839-1294, 867-1446, 876-1051, 885-1258, 989-1232, 1009-1159, 1025-1295, 1047- 1310, 1047-1510, 1052-1364, 1052-1376, 1064-1259, 1078-1688, 1081-1499, 1098-1375, 1159-1705, 1177-1435, 1204-1630, 1212-1467, 1251-1600, 1322-1941, 1373-1649, 1374-1659, 1459-1583, 1473-1723, 1483-1758, 1483- 1960, 1485-1815, 1500-1750, 1509-1774, 1513-2193, 1527-1793, 1528-1815, 1533-1898, 1540-1934, 1559-2130, 1563-2175, 1566-2197, 1594-1811, 1600-2145, 1614-1837, 1651-1868, 1661-1956, 1664-2032, 1674-1811, 1683- 1884, 1693-2236, 1709-1851, 1719-2243, 1743-2195, 1747-2206, 1751-2006, 1761-2015, 1776-2225, 1781-2225, 1783-2047, 1783-2067, 1783-2225, 1784-2225, 1788-2089, 1788-2101, 1788-2149, 1788-2177, 1791-2080, 1795- 2270, 1800-2225, 1801-2214, 1802-2258, 1816-2225, 1817-2151, 1819-2225, 1822-2225, 1825-2225, 1831-2089, 1831-2225, 1837-2225, 1841-2208, 1850-2225, 1852-2206, 1854-2225, 1855-2225, 1861-2225, 2003-2225 48/5515030CB1/ 1-667, 3-666, 572-1593, 646-1353, 646-1367, 646-1401, 646-1407, 646-1409, 646-1416, 646-1422, 646-1426, 646- 1593 1427, 646-1445, 646-1446, 901-1591, 939-1581, 999-1447, 1109-1402, 1115-1447, 1147-1447 49/1681532CB1/ 1-351, 1-543, 1-633, 1-2420, 5-296, 9-850, 278-562, 393-996, 450-996, 645-1311, 667-2440, 780-1449, 1368-1463, 2440 1370-1463, 1563-1675, 1563-2057 50/70845770CB1/ 1-694, 1-821, 8-628, 8-802, 9-802, 13-690, 17-716, 18-660, 21-802, 24-748, 26-748, 26-805, 27-742, 28-700, 30- 1329 636, 30-726, 30-730, 30-768, 30-781, 35-716, 38-802, 48-692, 55-657, 56-802, 85-612, 94-730, 118-733, 214-802, 247-677, 247-683, 247-696, 247-711, 247-723, 247-733, 247-787, 247-802, 275-802, 281-800, 284-802, 297-802. 320-638, 348-802, 355-710, 385-863, 394-802, 442-997, 450-793, 458-1264, 467-1194, 473-1329, 553-1131, 805- 857 51/3448184CB1/ 1-343, 266-825, 266-895, 267-524, 352-849, 352-882, 352-902, 535-1139, 535-1149, 850-1003, 856-1398, 859- 6311 1398, 1046-1398, 1177-1825, 1678-1923, 1779-2306, 1980-2306, 2100-2306, 2235-2303, 2235-2425, 2304-2456, 2347-2561, 2511-3270, 2745-2996, 2745-3270, 2752-3326, 2805-3275, 2996-3451, 3204-3501, 3234-3785, 3238- 3426, 3324-3981, 3440-3744, 3639-4028, 3988-4631, 4176-4361, 4179-4636, 4179-4640, 4186-4355, 4186-4428, 4186-4566, 4193-4640, 4291-4901, 4291-4906, 4310-4485, 4414-4538, 4487-4817, 4558-4640, 4565-5225, 4572- 4640, 4599-4640, 4641-4741, 4964-5438, 5065-5664, 5075-5157, 5209-5614, 5211-5889, 5410-5757, 5465-5731, 5469-5588, 5578-5806, 5597-5813, 5597-5874, 5605-5945, 5652-6311, 5690-5937, 5700-5834, 5700-5877, 5707- 5979, 5707-5988, 5727-5802, 5734-5981, 5734-6040, 5736-6092, 5747-5991 52/6322968CB1/ 1-856, 588-1035, 588-1095, 589-1414, 590-986, 590-991, 590-1081, 590-1091, 590-1228, 590-1353, 592-1016, 594- 2238 1073, 594-1161, 594-1296, 594-1317, 595-1074, 597-990, 597-1273, 601-1403, 604-932, 604-1153, 645-1116, 719- 1354, 844-1412, 878-1327, 884-1679, 1008-1372, 1039-1681, 1100-1817, 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1627-2271, 1628-2024, 1633-2046, 1633-2075, 1633-2217, 1637-2089, 1648- 2304, 1667-2314, 1672-2030, 1675-2282, 1694-2027, 1696-2306, 1697-2026, 1706-2220, 1719-2017, 1720-2122, 1722-2194, 1741-1998, 1747-2268, 1758-2332, 1793-2297, 1805-2199, 1816-2182, 1826-2094, 1826-2330, 1833- 2330, 1859-2559, 1913-2169, 1913-2291, 2001-2297, 2023-2283, 2028-2299, 2100-2343, 2112-2353, 2114-2242, 2114-2329, 2119-2297, 2120-2353 90/7510676CB1/ 1-209, 1-241, 1-256, 1-280, 1-523, 1-563, 1-586, 1-2020, 2-236, 2-399, 2-427, 2-520, 2-537, 2-552, 2-570, 2-573, 2- 2025 720, 3-562, 3-620, 13-298, 14-316, 22-303, 24-749, 29-711, 81-749, 93-624, 117-657, 162-720, 207-756, 208-617, 211-714, 221-826, 244-633, 246-699, 247-476, 253-564, 257-575, 264-857, 273-618, 342-919, 343-622, 345-928, 347-678, 347-824, 347-902, 348-875, 348-969, 354-881, 363-1062, 381-820, 388-945, 394-1055, 406-993, 411-533, 420-599, 421-968, 424-944, 426-967, 430-914, 434-986, 436-950, 90 439-825, 442-1036, 444-840, 445-965, 445-969, 446-984, 454-766, 459-1036, 467-1049, 470-1198, 489-1132, 490- 993, 496-893, 498-954, 517-764, 517-970, 538-986, 562-821, 567-999, 604-989, 620-1170, 622-1200, 627-1185, 628-718, 633-1316, 635-1115, 645-1302, 671-1209, 688-1348, 694-1176, 696-1172, 703-1258, 705-1297, 710-1287, 712-1313, 713-1348, 714-788, 723-1301, 767-1302, 782-1337, 784-1337, 788-930, 797-1195, 797-1322, 828-1275, 855-1277, 856-1311, 857-1341, 877-1100, 877-1327, 1059-1317, 1062-1315, 1072-1315, 1082-1341, 1088-1348, 1089-1345, 1089-1348, 1126-1380, 1177-1267, 1347-1897, 1347-1900, 1372-1892, 1380-1949, 1382-1968, 1385- 1841, 1400-1843, 1400-1949, 1404-1876, 1411-1800, 1415-1869, 1424-2018, 1430-1666, 1431-1629, 1433-1687, 1438-1848, 1447-1708, 1471- 2020, 1472-1799, 1482-1725, 1485-2020, 1504-1968, 1507-1966, 1514-1747, 1526-2018, 1534-1942, 1537-2004, 1554-1810, 1562-2005, 1572-2020, 1574-1966, 1575-2020, 1576-2020, 1594-1795, 1598-2020, 1599-2011, 1605- 1967, 1606-1866, 1624-2020, 1644-2012, 1648-2013, 1653-2008, 1702-1927, 1711-1973, 1717-1982, 1719-1888, 1719-2022, 1750-2005, 1776-1968, 1781-2009, 1793-1989, 1799-2025, 1824-2008, 1829-2020, 1840-2019, 1850- 2023, 1856-2024, 1872-2009, 1899-2015, 1909-2006

TABLE 5 Polynucleotide SEQ Incyte Representative ID NO: Project ID: Library 46 2562907CB1 SKIRNOR01 47 3744219CB1 LUNGDIS03 48 5515030CB1 TESTNOT11 49 1681532CB1 UTREDME06 50 70845770CB1 BRAIUNF01 51 3448184CB1 BRAWTDR02 52 6322968CB1 SMCRUNE01 53 6819485CB1 SINTFER02 54 7499882CB1 SINTNOR01 55 6623259CB1 TESTTUT02 56 2239208CB1 SINTFER02 57 3821431CB1 BONSTUT01 58 6973721CB1 BRAUTDR02 59 7499694CB1 BONSTUT01 60 2454570CB1 GBLADIT01 61 6595652CB1 SINTFEF03 62 5770223CB1 THYMNOR02 63 7729840CB1 SMCCNON03 64 4635167CB1 HELATXT04 65 7499571CB1 TESTNOT03 66 8047234CB1 BRATDIC01 67 8217739CB1 SPLNNOT04 68 413973CB1 BRSTNOT01 69 7501022CB1 BRAUNOR01 70 182852CB1 BRAUNOR01 71 1644979CB1 BRAUNOR01 72 55111748CB1 BRAHTDR03 73 3358362CB1 BRSTNOT09 74 8113230CB1 PKINDNV28 75 1785616CB1 PITUDIR01 76 71113255CB1 THP1NOT03 77 7502098CB1 PITUDIR01 78 7502099CB1 SKIRNOR01 79 7502100CB1 BRAITDR03 80 7502750CB1 PITUDIR01 81 7502891CB1 PITUDIR01 82 2571532CB1 STOMFET02 83 6436087CB1 PROTDNV02 84 7502109CB1 PITUDIR01 85 7500262CB1 HNT2AGT01 86 2172094CB1 KIDNFET01 87 7413862CB1 TESTTUT03 88 7503755CB1 THYMNOR02 89 7500488CB1 BRABDIR01 90 7510676CB1 OVARTUT10

TABLE 6 Library Vector Library Description BONSTUT01 pINCY Library was constructed using RNA isolated from sacral bone tumor tissue removed from an 18-year-old Caucasian female during an exploratory laparotomy with soft tissue excision. Pathology indicated giant cell tumor of the sacrum. Patient history included a soft tissue malignant neoplasm. Family history included prostate cancer. BRABDIR01 pINCY Library was constructed using RNA isolated from diseased cerebellum tissue removed from the brain of a 57-year-old Caucasian male, who died from a cerebrovascular accident. Patient history included Huntington's disease, emphysema, and tobacco abuse. BRAHTDR03 PCDNA2.1 This random primed library was constructed using RNA isolated from archaecortex, anterior hippocampus tissue removed from a 55-year-old Caucasian female who died from cholangiocarcinoma. Pathology indicated mild meningeal fibrosis predominately over the convexities, scattered axonal spheroids in the white matter of the cingulate cortex and the thalamus, and a few scattered neurofibrillary tangles in the entorhinal cortex and the periaqueductal gray region. Pathology for the associated tumor tissue indicated well-differentiated cholangiocarcinoma of the liver with residual or relapsed tumor. Patient history included cholangiocarcinoma, post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax, dehydration, malnutrition, oliguria and acute renal failure. Previous surgeries included cholecystectomy and resection of 85% of the liver. BRAITDR03 PCDNA2.1 This random primed library was constructed using RNA isolated from allocortex, cingulate posterior tissue removed from a 55-year-old Caucasian female who died from cholangiocarcinoma. Pathology indicated mild meningeal fibrosis predominately over the convexities, scattered axonal spheroids in the white matter of the cingulate cortex and the thalamus, and a few scattered neurofibrillary tangles in the entorhinal cortex and the periaqueductal gray region. Pathology for the associated tumor tissue indicated well-differentiated cholangiocarcinoma of the liver with residual or relapsed tumor. Patient history included cholangiocarcinoma, post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax, dehydration, malnutrition, oliguria and acute renal failure. Previous surgeries included cholecystectomy and resection of 85% of the liver. BRAIUNF01 pRARE This 5′ cap isolated full-length library was constructed using RNA isolated from a DU 145 cell line derived from a brain tumor removed from a 69-year-old Caucasian male. The cells were untreated for 14 hours. Pathology indicated metastatic carcinoma. Patient history included lymphocytic leukemia for 3 years and prostate carcinoma with metastasis to the brain. BRATDIC01 pINCY This large size-fractionated library was constructed using RNA isolated from diseased brain tissue removed from the left temporal lobe of a 27-year-old Caucasian male during a brain lobectomy. Pathology for the left temporal lobe, including the mesial temporal structures, indicated focal, marked pyramidal cell loss and gliosis in hippocampal sector CA1, consistent with mesial temporal sclerosis. The left frontal lobe showed a focal deep white matter lesion, characterized by marked gliosis, calcifications, and hemosiderin-laden macrophages, consistent with a remote perinatal injury. The frontal lobe tissue also showed mild to moderate generalized gliosis, predominantly subpial and subcortical, consistent with chronic seizure disorder. GFAP was positive for astrocytes. The patient presented with intractable epilepsy, focal epilepsy, hemiplegia, and an unspecified brain injury. Patient history included cerebral palsy, abnormality of gait, depressive disorder, and tobacco abuse in remission. Previous surgeries included tendon transfer. Patient medications included minocycline hydrochloride, Tegretol, phenobarbital, vitamin C, Pepcid, and Pevaryl. Family history included brain cancer in the father. BRAUNOR01 pINCY This random primed library was constructed using RNA isolated from striatum, globus pallidus and posterior putamen tissue removed from an 81-year-old Caucasian female who died from a hemorrhage and ruptured thoracic aorta due to atherosclerosis. Pathology indicated moderate atherosclerosis involving the internal carotids, bilaterally; microscopic infarcts of the frontal cortex and hippocampus; and scattered diffuse amyloid plaques and neurofibrillary tangles, consistent with age. Grossly, the leptomeninges showed only mild thickening and hyalinization along the superior sagittal sinus. The remainder of the leptomeninges was thin and contained some congested blood vessels. Mild atrophy was found mostly in the frontal poles and lobes, and temporal lobes, bilaterally. Microscopically, there were pairs of Alzheimer type II astrocytes within the deep layers of the neocortex. There was increased satellitosis around neurons in the deep gray matter in the middle frontal cortex. The amygdala contained rare diffuse plaques and neurofibrillary tangles. The posterior hippocampus contained a microscopic area of cystic cavitation with hemosiderin-laden macrophages surrounded by reactive gliosis. Patient history included sepsis, cholangitis, post-operative atelectasis, pneumonia CAD, cardiomegaly due to left ventricular hypertrophy, splenomegaly, arteriolonephrosclerosis, nodular colloidal goiter, emphysema, CHF, hypothyroidism, and peripheral vascular disease. BRAUTDR02 PCDNA2.1 This random primed library was constructed using RNA isolated from pooled amygdala and entorhinal cortex tissue removed from a 55-year-old Caucasian female who died from cholangiocarcinoma. Pathology indicated mild meningeal fibrosis predominately over the convexities, scattered axonal spheroids in the white matter of the cingulate cortex and the thalamus, and a few scattered neurofibrillary tangles in the entorhinal cortex and the periaqueductal gray region. Pathology for the associated tumor tissue indicated well-differentiated cholangiocarcinoma of the liver with residual or relapsed tumor. Patient history included cholangiocarcinoma, post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax, dehydration, malnutrition, oliguria and acute renal failure. Previous surgeries included cholecystectomy and resection of 85% of the liver. BRAWTDR02 PCDNA2.1 This random primed library was constructed using RNA isolated from dentate nucleus tissue removed from a 55-year-old Caucasian female who died from cholangiocarcinoma. Pathology indicated mild meningeal fibrosis predominately over the convexities, scattered axonal spheroids in the white matter of the cingulate cortex and the thalamus, and a few scattered neurofibrillary tangles in the entorhinal cortex and the periaqueductal gray region. Pathology for the associated tumor tissue indicated well-differentiated cholangiocarcinoma of the liver with residual or relapsed tumor. Patient history included cholangiocarcinoma, post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax, dehydration, malnutrition, oliguria and acute renal failure. Previous surgeries included cholecystectomy and resection of 85% of the liver. BRSTNOT01 PBLUESCRIPT Library was constructed using RNA isolated from the breast tissue of a 56-year-old Caucasian female who died in a motor vehicle accident. BRSTNOT09 pINCY Library was constructed using RNA isolated from breast tissue removed from a 45-year-old Caucasian female during unilateral extended simple mastectomy. Pathology for the associated tumor tissue indicated invasive nuclear grade 2-3 adenocarcinoma, with 3 of 23 lymph nodes positive for metastatic disease. Immunostains for estrogen/progesterone receptors were positive, and uninvolved tissue showed proliferative changes. The patient concurrently underwent a total abdominal hysterectomy. Patient history included valvuloplasty of mitral valve without replacement, rheumatic mitral insufficiency, and rheumatic heart disease. Family history included acute myocardial infarction, atherosclerotic coronary artery disease, and type II diabetes. GBLADIT01 pINCY The library was constructed using RNA isolated from diseased gallbladder tissue removed from a 18-year-old Caucasian female during cholecystectomy and incidental appendectomy. Pathology indicated acute and chronic cholecystitis with cholelithiasis. The gallbladder contained multiple fragments of stony material. The appendix showed lymphoid hyperplasia. The patient presented with abdominal pain, nausea, and vomiting. Patient history included Chlamydia, extrinsicasthma, and cesarean delivery (×3). Family history included benign hypertension, acute myocardial infarction, and atherosclerotic coronary artery disease. HELATXT04 pINCY Library was constructed using RNA isolated from a treated HeLa cell line, derived from cervical adenocarcinoma removed from a 31-year-old Black female. The cells were treated with 1 microM 5-aza-2′-deoxycytidine for 72 hours. HNT2AGT01 PBLUESCRIPT Library was constructed at Stratagene (STR937233), using RNA isolated from the hNT2 cell line derived from a human teratocarcinoma that exhibited properties characteristic of a committed neuronal precursor. Cells were treated with retinoic acid for 5 weeks and with mitotic inhibitors for two weeks and allowed to mature for an additional 4 weeks in conditioned medium. KIDNFET01 pINCY Library was constructed using RNA isolated from kidney tissue removed from a Caucasian female fetus, who died at 17 weeks' gestation from anencephalus. LUNGDIS03 pINCY Library was constructed using diseased lung tissue. 0.76 million clones from a diseased lung tissue library were subjected to two rounds of subtraction hybridization with 5.1 million clones from a normal lung tissue library. The starting library for subtraction was constructed using polyA RNA isolated from diseased lung tissue. Patient history included idiopathic pulmonary disease. Subtractive hybridization conditions were based on the methodologies of Swaroop et al. (1991) Nucleic Acids Res. 19: 1954; and Bonaldo et al. Genome Res. (1996) 6: 791. OVARTUT10 pINCY Library was constructed using RNA isolated from ovarian tumor tissue removed from the left ovary of a 58-year-old Caucasian female during a total abdominal hysterectomy, removal of a solitary ovary, and repair of inguinal hernia. Pathology indicated a metastatic grade 3 adenocarcinoma of colonic origin, forming a partially cystic and necrotic tumor mass in the left ovary, and an adenocarcinoma of colonic origin, forming a nodule in the left mesovarium. A single intramural leiomyoma was identified in the myometrium. The cervix showed mild chronic cystic cervicitis. Patient history included benign hypertension, follicular cyst of the ovary, colon cancer, benign colon neoplasm, and osteoarthritis. Family history included emphysema, myocardial infarction, atherosclerotic coronary artery disease, benign hypertension, and hyperlipidemia. PITUDIR01 PCDNA2.1 This random primed library was constructed using RNA isolated from pituitary gland tissue removed from a 70-year-old female who died from metastatic adenocarcinoma. PKINDNV28 PCR2-TOPOTA Library was constructed using pooled cDNA from different donors. cDNA was generated using mRNA isolated from pooled skeletal muscle tissue removed from ten 21 to 57-year-old Caucasian male and female donors who died from sudden death; from pooled thymus tissue removed from nine 18 to 32-year-old Caucasian male and female donors who died from sudden death; from pooled liver tissue removed from 32 Caucasian male and female fetuses who died at 18-24 weeks gestation due to spontaneous abortion; from kidney tissue removed from 59 Caucasian male and female fetuses who died at 20-33 weeks gestation due to spontaneous abortion; and from brain tissue removed from a Caucasian male fetus who died at 23 weeks gestation due to fetal demise. PROTDNV02 PCR2-TOPOTA Library was constructed using pooled cDNA from different donors. cDNA was generated using mRNA isolated from pooled small intestine tissue removed from a Caucasian male fetus (donor A) who died at 23 weeks' gestation from premature birth; from lung tissue removed from a Caucasian male fetus (donor B) who died from fetal demise; from pleura tumor tissue removed from a 55-year-old Caucasian female (donor C) during a complete pneumonectomy; from frontal/parietal brain tumor tissue removed from a 2-year-old Caucasian female (donor D) during excision of cerebral meningeal lesion; from liver tumor tissue removed from a 72-year-old Caucasian male (donor E) during partial hepatectomy; from pooled fetal brain tissue removed from a Caucasian male fetus (donor F) who was stillborn with a hypoplastic left heart at 23 weeks' gestation and from brain tissue removed from a Caucasian male fetus (donor G), who died at 23 weeks' gestation from premature birth; from pooled fetal kidney tissue removed from 59, 20-33-week-old male and female fetuses who died from spontaneous abortion; from pooled thymus tissue removed from 9, 18-32-year- old male and female donors who died from sudden death; and from pooled fetal liver tissue removed from 32, 18-24-week-old male and female fetuses. For donor A, serologies were negative. Family history included diabetes in the mother. For donor B, Serologies were negative. For donor C, pathology indicated grade 3 sarcoma most consistent with leiomyosarcoma, uterine primary, forming a bosellated mass replacing the right lower lobe and a portion of the middle lobe. Multiple nodules comprising the tumor show near total necrosis. Smooth muscle actin was positive. Estrogen PROTDNV02 receptor was negative and progesterone receptor was positive. The patient presented with shortness of breath. Patient history included peptic ulcer disease, normal delivery, anemia, and tobacco abuse in remission. Previous surgeries included total abdominal hysterectomy, bilateral salpingo-oophorectomy, hemorrhoidectomy, endoscopic excision of lung lesion, and appendectomy. Patient medications included Megace, tamoxifen, and Pepcid. Family history included multiple sclerosis in the mother; atherosclerotic coronary artery disease and type II diabetes in the father; and breast cancer in the grandparent(s). For donor D, pathology indicated neuroectodermal tumor with advanced ganglionic differentiation. The lesion was only moderately cellular but was mitotically active with a high MIB-1 labelling index. Neuronal differentiation was widespread and advanced. Multinucleate and dysplastic- appearing forms were readily seen. The glial element was less prominent. The patient presented with motor seizures. Family history included hypertension in the grandparent(s). For donor E, pathology indicated metastatic grade 2 (of 4) neuroendocrine carcinoma forming a mass. The patient presented with metastatic liver cancer. Patient history included benign hypertension, type I diabetes, prostatic hyperplasia, prostate cancer, alcohol abuse in remission, and tobacco abuse in remission. Previous surgeries included destruction of a pancreatic lesion, closed prostatic biopsy, transurethral prostatectomy, removal of bilateral testes and total splenectomy. Patient medications included Eulexin, Hytrin, Proscar, Ecotrin, and insulin. Family history included atherosclerotic coronary artery disease and acute myocardial infarction in the mother; atherosclerotic coronary artery disease and type II diabetes in the father. For donor F and G, Serologies were negative for both donors and family history for donor G included diabetes in the mother. SINTFEF03 PCMV-ICIS This full-length enriched library was constructed using RNA isolated from small intestine tissue removed from a Caucasian male fetus, who died at 23 weeks' gestation from premature birth. Serologies were negative. Family history included diabetes in the mother. SINTFER02 pINCY This random primed library was constructed using RNA isolated from small intestine tissue removed from a Caucasian male fetus who died from fetal demise. SINTNOR01 PCDNA2.1 This random primed library was constructed using RNA isolated from small intestine tissue removed from a 31-year-old Caucasian female during Roux-en-Y gastric bypass. Patient history included clinical obesity. SKIRNOR01 PCDNA2.1 This random primed library was constructed using RNA isolated from skin tissue removed from the breast of a 17-year-old Caucasian female during bilateral reduction mammoplasty. Patient history included breast hypertrophy. Family history included benign hypertension. SMCCNON03 pINCY This normalized smooth muscle cell library was constructed from 7.56 million independent clones from a smooth muscle cell library. Starting RNA was made from smooth muscle cell tissue removed from the coronary artery of a 3-year-old Caucasian male. The normalization and hybridization conditions were adapted from Soares et al., (PNAS (1994) 91: 9228-9232); Swaroop et al., (NAR (1991) 19: 1954); and Bonaldo et al., (Genome Research (1996) 6: 791-806), using a significantly longer (48 hour) reannealing hybridization period. SMCRUNE01 PCDNA2.1 This 5′ biased random primed library was constructed using RNA isolated from untreated smooth muscle cell tissue removed from the renal vein of a 57-year-old Caucasian male. SPLNNOT04 pINCY Library was constructed using RNA isolated from the spleen tissue of a 2-year-old Hispanic male, who died from cerebral anoxia. Past medical history and serologies were negative. STOMFET02 pINCY Library was constructed using RNA isolated from stomach tissue removed from a Hispanic male fetus, who died at 18 weeks' gestation. TESTNOT03 PBLUESCRIPT Library was constructed using RNA isolated from testicular tissue removed from a 37-year-old Caucasian male, who died from liver disease. Patient history included cirrhosis, jaundice, and liver failure. TESTNOT11 pINCY Library was constructed using RNA isolated from testicular tissue removed from a 16-year-old Caucasian male who died from hanging. Patient history included drug use (tobacco, marijuana, and cocaine use), and medications included Lithium, Ritalin, and Paxil. TESTTUT02 pINCY Library was constructed using RNA isolated from testicular tumor removed from a 31-year-old Caucasian male during unilateral orchiectomy. Pathology indicated embryonal carcinoma. TESTTUT03 pINCY Library was constructed using RNA isolated from right testicular tumor tissue removed from a 45-year-old Caucasian male during a unilateral orchiectomy. Pathology indicated seminoma. Patient history included hyperlipidemia and stomach ulcer. Family history included cerebrovascular disease, skin cancer, hyperlipidemia, acute myocardial infarction, and atherosclerotic coronary artery disease. THP1NOT03 pINCY Library was constructed using RNA isolated from untreated THP-1 cells. THP-1 is a human promonocyte line derived from the peripheral blood of a 1-year-old Caucasian male with acute monocytic leukemia (ref: Int. J. Cancer (1980) 26: 171). THYMNOR02 pINCY The library was constructed using RNA isolated from thymus tissue removed from a 2-year-old Caucasian female during a thymectomy and patch closure of left atrioventricular fistula. Pathology indicated there was no gross abnormality of the thymus. The patient presented with congenital heart abnormalities. Patient history included double inlet left ventricle and a rudimentary right ventricle, pulmonary hypertension, cyanosis, subaortic stenosis, seizures, and a fracture of the skull base. Family history included reflux neuropathy. UTREDME06 PCDNA2.1 This 5′ biased random primed library was constructed using RNA isolated from endometrial tissue removed from a 32-year-old female. Pathology indicated severe cervical dysplasia (CIN III) focally involving the squamocolumnar junction at the 1, 6 and 7 o'clock positions. Mild koilocytotic dysplasia was identified elsewhere within the cervix.

TABLE 7 Parameter Program Description Reference Threshold ABI A program that removes vector sequences and Applied Biosystems, Foster City, CA. FACTURA masks ambiguous bases in nucleic acid sequences. ABI/ A Fast Data Finder useful in comparing and Applied Biosystems, Foster City, CA; Mismatch <50% PARACEL annotating amino acid or nucleic acid sequences. Paracel Inc., Pasadena, CA. FDF ABI A program that assembles nucleic acid sequences. Applied Biosystems, Foster City, CA. AutoAssembler BLAST A Basic Local Alignment Search Tool useful in Altschul, S. F. et al. (1990) J. Mol. Biol. ESTs: Probability sequence similarity search for amino acid and 215: 403-410; Altschul, S. F. et al. (1997) value = 1.0E−8 nucleic acid sequences. BLAST includes five Nucleic Acids Res. 25: 3389-3402. or less; functions: blastp, blastn, blastx, tblastn, Full Length sequences: and tblastx. Probability value = 1.0E−10 or less FASTA A Pearson and Lipman algorithm that searches Pearson, W. R. and D. J. Lipman (1988) Proc. ESTs: fasta E for similarity between a query sequence and a Natl. Acad Sci. USA 85: 2444-2448; Pearson, value = 1.06E−6 group of sequences of the same type. FASTA W. R. (1990) Methods Enzymol. 183: 63-98; Assembled ESTs: comprises as least five functions: fasta, and Smith, T. F. and M. S. Waterman (1981) fasta Identity = tfasta, fastx, tfastx, and ssearch. Adv. Appl. Math. 2: 482-489. 95% or greater and Match length = 200 bases or greater; fastx E value = 1.0E−8 or less; Full Length sequences: fastx score = 100 or greater BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S. and J. G. Henikoff (1991) Probability value = sequence against those in BLOCKS, PRINTS, Nucleic Acids Res. 19: 6565-6572; Henikoff, 1.0E−3 or less DOMO, PRODOM, and PFAM databases to search J. G. and S. Henikoff (1996) Methods for gene families, sequence homology, and Enzymol. 266: 88-105; and Attwood, T. K. et structural fingerprint regions. al. (1997) J. Chem. Inf. Comput. Sci. 37: 417-424. HMMER An algorithm for searching a query sequence Krogh, A. et al. (1994) J. Mol. Biol. PFAM, INCY, SMART against hidden Markov model (HMM)-based 235: 1501-1531; Sonnhammer, E. L. L. et al. or TIGRFAM hits: databases of protein family consensus (1988) Nucleic Acids Res. 26: 320-322; Probability sequences, such as PFAM, INCY, SMART, Durbin, R. et al. (1998) Our World View, in value = 1.0E−3 and TIGRFAM. a Nutshell, Cambridge Univ. Press, pp. or less; 1-350. Signal peptide hits: Score = 0 or greater ProfileScan An algorithm that searches for structural and Gribskov, M. et al. (1988) CABIOS 4: 61-66; Normalized quality sequence motifs in protein sequences that match Gribskov, M. et al. (1989) Methods score ≧ GCG- sequence patterns defined in Prosite. Enzymol. 183: 146-159; Bairoch, A. et al. specified “HIGH” (1997) Nucleic Acids Res. 25: 217-221. value for that particular Prosite motif. Generally, score = 1.4-2.1. Phred A base-calling algorithm that examines Ewing, B. et al. (1998) Genome Res. 8: automated sequencer traces with high 175-185; Ewing, B. and P. Green (1998) sensitivity and probability. Genome Res. 8: 186-194. Phrap A Phils Revised Assembly Program including Smith, T. F. and M. S. Waterman (1981) Adv. Score = 120 or SWAT and CrossMatch, programs based on Appl. Math. 2: 482-489; Smith, T. F. and greater; efficient implementation of the Smith-Waterman M. S. Waterman (1981) J. Mol. Biol. 147: Match length = algorithm, useful in searching sequence 195-197; and Green, P., University of 56 or greater homology and assembling DNA sequences. Washington, Seattle, WA. Consed A graphical tool for viewing and editing Phrap Gordon, D. et al. (1998) Genome Res. 8: assemblies. 195-202. SPScan A weight matrix analysis program that scans Nielson, H. et al. (1997) Protein Engineering Score = 3.5 protein sequences for the presence of secretory 10: 1-6; Claverie, J. M. and S. Audic (1997) or greater signal peptides. CABIOS 12: 431-439. TMAP A program that uses weight matrices to Persson, B. and P. Argos (1994) J. Mol. Biol. delineate transmembrane segments on protein 237: 182-192; Persson, B. and P. Argos sequences and determine orientation. (1996) Protein Sci. 5: 363-371. TMHMMER A program that uses a hidden Markov model (HMM) Sonnhammer, E. L. et al. (1998) Proc. Sixth to delineate transmembrane segments on protein Intl. Conf. On Intelligent Systems for Mol. sequences and determine orientation. Biol., Glasgow et al., eds., The Am. Assoc. for Artificial Intelligence Press, Menlo Park, CA, pp. 175-182. Motifs A program that searches amino acid sequences for Bairoch, A. et al. (1997) Nucleic Acids Res. patterns that matched those defined in Prosite. 25: 217-221; Wisconsin Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, WI.

TABLE 8 Caucasian African Asian Hispanic SEQ Allele 1 Allele 1 Allele 1 Allele 1 ID EST CB1 EST Allele Allele Amino fre- fre- fre- fre- NO: PID EST ID SNP ID SNP SNP Allele 1 2 Acid quency quency quency quency 90 7510676 1431290F6 SNP00047730 302 1178 C C T P356 0.9 0.68 n/d 0.85 90 7510676 1537694H1 SNP00058550 97 1889 C C T noncoding n/a n/a n/a n/a 90 7510676 1694022T6 SNP00058550 57 1890 C C T noncoding n/a n/a n/a n/a 90 7510676 1695368T6 SNP00058550 64 1896 C C T noncoding n/a n/a n/a n/a 90 7510676 2280709F6 SNP00014421 65 63 C C G noncoding n/a n/a n/a n/a 90 7510676 2280709T6 SNP00058550 49 1913 C C T noncoding n/a n/a n/a n/a 90 7510676 2699414F6 SNP00014422 546 548 G G A A146 n/d n/a n/a n/a 90 7510676 3524028H1 SNP00014423 283 989 C C T H293 0.52 n/a n/a n/a 90 7510676 3524753H1 SNP00027367 192 1279 A G A S389 n/a n/a n/a n/a 90 7510676 7716967H1 SNP00014423 119 990 T C T F293 0.52 n/a n/a n/a 

1. An isolated polypeptide selected from the group consisting of: a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-3, SEQ ID NO:6-8, SEQ ID NO:10, SEQ ID NO:12-15, SEQ ID NO:17-22, SEQ ID NO:25-28, SEQ ID NO:31, SEQ ID NO:36-38, and SEQ ID NO:40-43, c) a polypeptide comprising a naturally occurring amino acid sequence at least 99% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:4 and SEQ ID NO:33-34, d) a polypeptide comprising a naturally occurring amino acid sequence at least 98% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:29-30, SEQ ID NO:32, SEQ ID NO:39, and SEQ ID NO:45, e) a polypeptide comprising a naturally occurring amino acid sequence at least 94% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:9, SEQ ID NO:16, and SEQ ID NO:44, f) a polypeptide comprising a naturally occurring amino acid sequence at least 96% identical to the amino acid sequence of SEQ ID NO:11, g) a polypeptide comprising a naturally occurring amino acid sequence at least 91% identical to the amino acid sequence of SEQ ID NO:23, h) a polypeptide comprising a naturally occurring amino acid sequence at least 92% identical to the amino acid sequence of SEQ ID NO:24, i) a polypeptide comprising a naturally occurring amino acid sequence at least 97% identical to the amino acid sequence of SEQ ID NO:35, j) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45, and k) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-45.
 2. An isolated polypeptide of claim 1 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-45.
 3. An isolated polynucleotide encoding a polypeptide of claim
 1. 4. An isolated polynucleotide encoding a polypeptide of claim
 2. 5. An isolated polynucleotide of claim 4 comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90.
 6. A recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim
 3. 7. A cell transformed with a recombinant polynucleotide of claim
 6. 8. (canceled)
 9. A method of producing a polypeptide of claim 1, the method comprising: a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide, and said recombinant polynucleotide comprises a promoter sequence operably linked to a polynucleotide encoding the polypeptide of claim 1, and b) recovering the polypeptide so expressed.
 10. A method of claim 9, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-45.
 11. An isolated antibody which specifically binds to a polypeptide of claim
 1. 12. An isolated polynucleotide selected from the group consisting of: a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-90, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:46-55 and SEQ ID NO:57-89, c) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 99% identical to the polynucleotide sequence of SEQ ID NO:56, d) a polynucleotide consisting essentially of a naturally occurring polynucleotide sequence at least 90% identical to the polynucleotide sequence of SEQ ID NO:90, e) a polynucleotide complementary to a polynucleotide of a), f) a polynucleotide complementary to a polynucleotide of b), g) a polynucleotide complementary to a polynucleotide of c), h) a polynucleotide complementary to a polynucleotide of d), and i) an RNA equivalent of a)-h).
 13. (canceled)
 14. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising: a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
 15. (canceled)
 16. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising: a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
 17. A composition comprising a polypeptide of claim 1 and a pharmaceutically acceptable excipient.
 18. A composition of claim 17, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-45.
 19. (canceled)
 20. A method of screening a compound for effectiveness as an agonist of a polypeptide of claim 1, the method comprising: a) exposing a sample comprising a polypeptide of claim 1 to a compound, and b) detecting agonist activity in the sample.
 21. (canceled)
 22. (canceled)
 23. A method of screening a compound for effectiveness as an antagonist of a polypeptide of claim 1, the method comprising: a) exposing a sample comprising a polypeptide of claim 1 to a compound, and b) detecting antagonist activity in the sample.
 24. (canceled)
 25. (canceled)
 26. A method of screening for a compound that specifically binds to the polypeptide of claim 1, the method comprising: a) combining the polypeptide of claim 1 with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide of claim 1 to the test compound, thereby identifying a compound that specifically binds to the polypeptide of claim
 1. 27. (canceled)
 28. A method of screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a sequence of claim 5, the method comprising: a) exposing a sample comprising the target polynucleotide to a compound, under conditions suitable for the expression of the target polynucleotide, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.
 29. A method of assessing toxicity of a test compound, the method comprising: a) treating a biological sample containing nucleic acids with the test compound, b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide of claim 12 under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide of claim 12 or fragment thereof, c) quantifying the amount of hybridization complex, and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound. 30-145. (canceled) 